-
1
-
-
1042298843
-
Computational design of protein-protein interactions
-
Kortemme T, Baker D (2004) Computational design of protein-protein interactions, Curr Opin Chem Biol, 8: 91–97
-
(2004)
Curr Opin Chem Biol
, vol.8
, pp. 91-97
-
-
Kortemme, T.1
Baker, D.2
-
2
-
-
2942582560
-
A structural perspective on protein-protein interactions
-
Russel RB, Alber F, Aloy P, Davis FP, Korkin D, Pichaud M, Topf M, Sali A (2004) A structural perspective on protein-protein interactions, Curr Opin Struct Biol, 14: 313–324
-
(2004)
Curr Opin Struct Biol
, vol.14
, pp. 313-324
-
-
Russel, R.B.1
Alber, F.2
Aloy, P.3
Davis, F.P.4
Korkin, D.5
Pichaud, M.6
Topf, M.7
Sali, A.8
-
3
-
-
1942487741
-
Computational analysis of ligand binding dynamics at the intermolecular hot spots with the aid of simulated tempering and binding free energy calculations
-
Verkhivker GM (2004) Computational analysis of ligand binding dynamics at the intermolecular hot spots with the aid of simulated tempering and binding free energy calculations, Mol J Graph Model, 22(5): 335–348
-
(2004)
Mol J Graph Model
, vol.22
, Issue.5
, pp. 335-348
-
-
Verkhivker, G.M.1
-
5
-
-
0028286471
-
Kinetics versus thermodynamics in protein folding
-
Baker D, Agard DA (1994) Kinetics versus thermodynamics in protein folding, Biochemistry, 33: 7505–7509
-
(1994)
Biochemistry
, vol.33
, pp. 7505-7509
-
-
Baker, D.1
Agard, D.A.2
-
6
-
-
0029364787
-
Conservation of water molecules in an antibody-antigen interaction
-
Braden BC, Poljak RJ(1995) Conservation of water molecules in an antibody-antigen interaction, Mol J Recogn, 9: 317–325
-
(1995)
Mol J Recogn
, vol.9
, pp. 317-325
-
-
Braden, B.C.1
Poljak, R.J.2
-
7
-
-
0029870875
-
Crystal structure of the complex of the variable domain of antibody D1.3 and the turkey egg with lysozyme: A novel conformational change in antibody CDF-L3 selects for antigen
-
Braden BC, Fields BA, Ysern X, Goldbaum FA, Dall’Acqua W, Schwartz FP, Poljak RJ, Mariuzza RA (1996) Crystal structure of the complex of the variable domain of antibody D1.3 and the turkey egg with lysozyme: a novel conformational change in antibody CDF-L3 selects for antigen, J Mol Biol, 257: 889–894
-
(1996)
J Mol Biol
, vol.257
, pp. 889-894
-
-
Braden, B.C.1
Fields, B.A.2
Ysern, X.3
Goldbaum, F.A.4
Dall’Acqua, W.5
Schwartz, F.P.6
Poljak, R.J.7
Mariuzza, R.A.8
-
8
-
-
0029764534
-
A mutational analysis of the binding of two different proteins to the same antibody
-
Dall’Acqua W, Goldman E, Eisenstein E, Mariuzza RA (1996) A mutational analysis of the binding of two different proteins to the same antibody, Biochemistry, 35: 9667–9676
-
(1996)
Biochemistry
, vol.35
, pp. 9667-9676
-
-
Dall’Acqua, W.1
Goldman, E.2
Eisenstein, E.3
Mariuzza, R.A.4
-
9
-
-
0032835617
-
De novo design and structural characterization of proteins and metalloproteins
-
DeGrado WF, Summa CM, Pavone V, Nastri F, Lombardi A (1999) De novo design and structural characterization of proteins and metalloproteins, Annu Rev Biochem, 68: 779–819
-
(1999)
Annu Rev Biochem
, vol.68
, pp. 779-819
-
-
Degrado, W.F.1
Summa, C.M.2
Pavone, V.3
Nastri, F.4
Lombardi, A.5
-
10
-
-
0000062094
-
Electrostatics in biomolecular structure and dynamics
-
Davis ME, Mccammon JA (1990) Electrostatics in biomolecular structure and dynamics, Chem Rev, 94: 7684
-
(1990)
Chem Rev
, vol.94
, pp. 7684
-
-
Davis, M.E.1
McCammon, J.A.2
-
11
-
-
0036323965
-
Ligand-induced changes in the binding sites of proteins
-
Frader X, de la Cruz X, CHTP Silva, Gelpi JL, Luque FJ and Orozco M(2002) Ligand-induced changes in the binding sites of proteins, Bioinformatics, 18(7): 939–948
-
(2002)
Bioinformatics
, vol.18
, Issue.7
, pp. 939-948
-
-
Frader, X.1
de la Cruz, X.2
Silva, C.H.T.P.3
Gelpi, J.L.4
Luque, F.J.5
Orozco, M.6
-
12
-
-
0033694923
-
De novo design of helical bundles as models for understanding protein folding and function
-
Hill RB, Raleigh DP, DeGrado WF (2000) De novo design of helical bundles as models for understanding protein folding and function, Acc Chem Res, 33: 745–754
-
(2000)
Acc Chem Res
, vol.33
, pp. 745-754
-
-
Hill, R.B.1
Raleigh, D.P.2
Degrado, W.F.3
-
13
-
-
0027966019
-
13C assignments and the three-dimensional solution structure of barstar using nuclear magnetic resonance spectroscopy
-
Lubienski MJ, Bycroft M, Freund SMV, Fersht AR (1994) 13C assignments and the three-dimensional solution structure of barstar using nuclear magnetic resonance spectroscopy, Biochemistry, 33: 8866–8877
-
(1994)
Biochemistry
, vol.33
, pp. 8866-8877
-
-
Lubienski, M.J.1
Bycroft, M.2
Freund, S.M.V.3
Fersht, A.R.4
-
14
-
-
84962439356
-
Roles of electrostatic interactions in proteins
-
Nakamura HQ (1996) Roles of electrostatic interactions in proteins, Rev Biophys, 29: 1–90
-
(1996)
Rev Biophys
, vol.29
, pp. 1-90
-
-
Nakamura, H.Q.1
-
16
-
-
0029056922
-
Energetics of protein-protein interactions: Analysis of the barnase-barstar interface by single mutations and double mutant cycles
-
Schreiber G, Fersht AR (1995) Energetics of protein-protein interactions: analysis of the barnase-barstar interface by single mutations and double mutant cycles, J Mol Biol, 248: 478–486
-
(1995)
J Mol Biol
, vol.248
, pp. 478-486
-
-
Schreiber, G.1
Fersht, A.R.2
-
17
-
-
0031191655
-
-
de Silva AP, Gunaratne HQN, Gunnlaugsson T, Huxley AJM, McCoy CP, Rademacher JT, Rice TE (1997) Chem Rev, 97: 1515
-
(1997)
Chem Rev
, vol.97
, pp. 1515
-
-
de Silva, A.P.1
Gunaratne, H.Q.N.2
Gunnlaugsson, T.3
Huxley, A.J.M.4
McCoy, C.P.5
Rademacher, J.T.6
Rice, T.E.7
-
18
-
-
0035847237
-
Imprinted chiral stationary phases in high-performance liquid chromatography
-
Review
-
Sellergren BJ (2001) Imprinted chiral stationary phases in high-performance liquid chromatography, Chromatogr A J, 906(1–2): 227–252, Review
-
(2001)
Chromatogr a J
, vol.906
, Issue.1-2
, pp. 227-252
-
-
Sellergren, B.J.1
-
19
-
-
0035891256
-
Retention and separation of adenosine and analogues by affinity chromatography with an aptamer stationary phase
-
Deng Q, German I, Buchanan D, Kennedy RT (2001) Retention and separation of adenosine and analogues by affinity chromatography with an aptamer stationary phase, Anal Chem, 73: 5415–5421
-
(2001)
Anal Chem
, vol.73
, pp. 5415-5421
-
-
Deng, Q.1
German, I.2
Buchanan, D.3
Kennedy, R.T.4
-
20
-
-
0028031316
-
The blind watchmaker and rational protein engineering
-
Anthonsen HW, Baptista A, Drablos F, Martel P, Petersen SB (1994) The blind watchmaker and rational protein engineering, J Biotechnol, 36: 185–220
-
(1994)
J Biotechnol
, vol.36
, pp. 185-220
-
-
Anthonsen, H.W.1
Baptista, A.2
Drablos, F.3
Martel, P.4
Petersen, S.B.5
-
22
-
-
0034725455
-
Modeling of the TCR-MHC-peptide complex, M
-
Michielin O, Luescher I, Karplus M (2000) Modeling of the TCR-MHC-peptide complex, M J Mol Biol, 300: 1205–1235
-
(2000)
J Mol Biol
, vol.300
, pp. 1205-1235
-
-
Michielin, O.1
Luescher, I.2
Karplus, M.3
-
23
-
-
0033915982
-
Recent advances in structure-based rational drug design
-
Gane PJ, Dean PM (2000) Recent advances in structure-based rational drug design, Curr Opin Struct Biol, 10: 401
-
(2000)
Curr Opin Struct Biol
, vol.10
, pp. 401
-
-
Gane, P.J.1
Dean, P.M.2
-
24
-
-
0029623184
-
Computational methods to predict binding free energy in ligand-receptor complexes
-
Ajay, Murcko MA (1995) Computational methods to predict binding free energy in ligand-receptor complexes, J Med Chem, 38: 4953–4967
-
(1995)
J Med Chem
, vol.38
, pp. 4953-4967
-
-
Ajay, M.M.A.1
-
25
-
-
0036890285
-
Binding affinity and specificity from computational studies
-
Lazaridis T (2002) Binding affinity and specificity from computational studies, Current Organic Chemistry, 6: 1319–1332
-
(2002)
Current Organic Chemistry
, vol.6
, pp. 1319-1332
-
-
Lazaridis, T.1
-
26
-
-
0032054612
-
Theory of Biomolecular Recognition
-
McCammon JA (1998) Theory of Biomolecular Recognition, Curr Opin Struct Biol, 8: 245
-
(1998)
Curr Opin Struct Biol
, vol.8
, pp. 245
-
-
McCammon, J.A.1
-
27
-
-
0000372879
-
Protein–protein interactions: Interface structure, binding thermodynamics and mutational analysis
-
Stites WE (1997) Protein–protein interactions: interface structure, binding thermodynamics and mutational analysis, Chem Rev, 97: 1233
-
(1997)
Chem Rev
, vol.97
, pp. 1233
-
-
Stites, W.E.1
-
29
-
-
0030040277
-
Interactions of protein antigens with antibodies
-
Davies DR, Cohen GH (1996) Interactions of protein antigens with antibodies, Proc Natl Acad Sci USA, 93: 7
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 7
-
-
Davies, D.R.1
Cohen, G.H.2
-
31
-
-
33646195474
-
The hydrogen bond in molecular recognition
-
Fersht AR (1987) The hydrogen bond in molecular recognition, Trends Biochem Sci, 12: 301–304
-
(1987)
Trends Biochem Sci
, vol.12
, pp. 301-304
-
-
Fersht, A.R.1
-
33
-
-
0026350498
-
Systematic mutational analyses of protein-protein interfaces
-
Wells JA (1991) Systematic mutational analyses of protein-protein interfaces, Methods Enzymol, 202: 390–411
-
(1991)
Methods Enzymol
, vol.202
, pp. 390-411
-
-
Wells, J.A.1
-
34
-
-
0027318516
-
Structure and function of human growth hormone: Implications for the hematopoietins
-
Wells JA, De Vos AM (1993) Structure and function of human growth hormone: implications for the hematopoietins, Annu Rev Biophys Biomol Struct, 22: 329–351
-
(1993)
Annu Rev Biophys Biomol Struct
, vol.22
, pp. 329-351
-
-
Wells, J.A.1
de Vos, A.M.2
-
35
-
-
0028260226
-
Structural and functional basis for hormone binding and receptor oligomerization
-
Wells JA (1994) Structural and functional basis for hormone binding and receptor oligomerization, Curr Opin Cell Biol, 6: 163–173
-
(1994)
Curr Opin Cell Biol
, vol.6
, pp. 163-173
-
-
Wells, J.A.1
-
36
-
-
0030050701
-
Binding in the growth hormone receptor complex
-
Wells JA (1996) Binding in the growth hormone receptor complex, Proc Natl Acad Sci USA, 93:1–6
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 1-6
-
-
Wells, J.A.1
-
37
-
-
0141815542
-
Computational detection of the binding-site hot spot at the remodelled human growth hormone-receptor interface
-
Verkhivker GM, Bouzida D, Gehlhaar DK, Rejto PA, Freer ST, Rose PM(2003) Computational detection of the binding-site hot spot at the remodelled human growth hormone-receptor interface, Proteins, 53: 201–219
-
(2003)
Proteins
, vol.53
, pp. 201-219
-
-
Verkhivker, G.M.1
Bouzida, D.2
Gehlhaar, D.K.3
Rejto, P.A.4
Freer, S.T.5
Rose, P.M.6
-
38
-
-
0035107854
-
The Hans Neurath Award lecture of The Protein Society: Proteins – A testament to physics, chemistry, and evolution
-
Thornton JM (2001) The Hans Neurath Award lecture of The Protein Society: proteins – A testament to physics, chemistry, and evolution, Protein Sci, 10: 3–11
-
(2001)
Protein Sci
, vol.10
, pp. 3-11
-
-
Thornton, J.M.1
-
39
-
-
0027132013
-
Comparison of a structural and functional epitope
-
Cunnigham BC, Wells JA (1993) Comparison of a structural and functional epitope, J Mol Biol, 234: 554–563
-
(1993)
J Mol Biol
, vol.234
, pp. 554-563
-
-
Cunnigham, B.C.1
Wells, J.A.2
-
40
-
-
0028916599
-
A hot spot of binding energy hormone-receptor interfaces
-
Clackson T, Wells JA (1995) A hot spot of binding energy hormone-receptor interfaces, Science, 267: 383–386
-
(1995)
Science
, vol.267
, pp. 383-386
-
-
Clackson, T.1
Wells, J.A.2
-
41
-
-
0003187567
-
The atomic structure of protein-protein recognition sites
-
Conte LL, Chothia C, Janin J (1999) The atomic structure of protein-protein recognition sites, J Mol Biol, 285: 2177–2198
-
(1999)
J Mol Biol
, vol.285
, pp. 2177-2198
-
-
Conte, L.L.1
Chothia, C.2
Janin, J.3
-
42
-
-
3142781225
-
Small-molecules inhibitors of protein-protein interactions: Progressing towards the dream
-
Arkin MR, Wells AJ (2004) Small-molecules inhibitors of protein-protein interactions: progressing towards the dream, Drug Discovery, 3: 301–317
-
(2004)
Drug Discovery
, vol.3
, pp. 301-317
-
-
Arkin, M.R.1
Wells, A.J.2
-
43
-
-
0037452709
-
Binding of small molecules to an adaptive protein–protein interface
-
Arkin MR, Randal M, DeLano WL, Hyde J, Luong TN, Oslob JD, Raphael DR, Taylor L, Wang J, McDowell RS, Wells JA, Braisted AC (2003) Binding of small molecules to an adaptive protein–protein interface, Proc Natl Acad Sci USA, 100: 1603–1608
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 1603-1608
-
-
Arkin, M.R.1
Randal, M.2
Delano, W.L.3
Hyde, J.4
Luong, T.N.5
Oslob, J.D.6
Raphael, D.R.7
Taylor, L.8
Wang, J.9
McDowell, R.S.10
Wells, J.A.11
Braisted, A.C.12
-
44
-
-
0032479179
-
Anatomy of hot spots in protein interfaces
-
Bogan AA, Thorn KS (1998) Anatomy of hot spots in protein interfaces, J Mol Biol, 280: 1–9
-
(1998)
J Mol Biol
, vol.280
, pp. 1-9
-
-
Bogan, A.A.1
Thorn, K.S.2
-
45
-
-
11844249426
-
Hot regions in protein-protein interactions: The organization and contribution of structurally conserved hot spot residues
-
Keskin O, Ma B, R Nussinov R (2005) Hot regions in protein-protein interactions: the organization and contribution of structurally conserved hot spot residues, J Mol Biol, 345: 1281–1294
-
(2005)
J Mol Biol
, vol.345
, pp. 1281-1294
-
-
Keskin, O.1
Ma, B.2
R Nussinov, R.3
-
46
-
-
0032958585
-
Energetic analysis of an antigen/antibody interface: alanine scanning mutagenesis and double mutant cycles on the HyHEL-100lysozyme interaction
-
Pons J, Rajpal A, Kirsch J (1999) Energetic analysis of an antigen/antibody interface: alanine scanning mutagenesis and double mutant cycles on the HyHEL-100lysozyme interaction, Protein Sci, 8: 958–968
-
(1999)
Protein Sci
, vol.8
, pp. 958-968
-
-
Pons, J.1
Rajpal, A.2
Kirsch, J.3
-
47
-
-
0030021877
-
Computational method for relative binding energies of enzyme-substrate complexes
-
Zhang T, Koshland DE (1996) Computational method for relative binding energies of enzyme-substrate complexes, Protein Sci, 5: 348–356
-
(1996)
Protein Sci
, vol.5
, pp. 348-356
-
-
Zhang, T.1
Koshland, D.E.2
-
49
-
-
0035186285
-
Free energies of protein decoys provide insight into determinants of protein stability
-
Vorobjev YN, Hermans J (2001) Free energies of protein decoys provide insight into determinants of protein stability, Protein Sci, 10: 2498–2506
-
(2001)
Protein Sci
, vol.10
, pp. 2498-2506
-
-
Vorobjev, Y.N.1
Hermans, J.2
-
50
-
-
0031872292
-
Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model
-
Vorobjev YN, Almagro JC, Hermans J (1998) Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model, Proteins, 32: 399–413
-
(1998)
Proteins
, vol.32
, pp. 399-413
-
-
Vorobjev, Y.N.1
Almagro, J.C.2
Hermans, J.3
-
51
-
-
0030861662
-
Identification of cooperative folding units in a set of native proteins
-
Wallqvist A, Smythers GW, Covel DG (1997) Identification of cooperative folding units in a set of native proteins, Protein Sci, 6: 1627–42
-
(1997)
Protein Sci
, vol.6
, pp. 1627-1642
-
-
Wallqvist, A.1
Smythers, G.W.2
Covel, D.G.3
-
52
-
-
0031285905
-
Deciphering the timescales and mechanisms of protein folding using minimal off-lattice models
-
Thirumalai D, Klimov DK, Woodson SA (1997) Deciphering the timescales and mechanisms of protein folding using minimal off-lattice models, Theor Chem Acc, 96: 14–22
-
(1997)
Theor Chem Acc
, vol.96
, pp. 14-22
-
-
Thirumalai, D.1
Klimov, D.K.2
Woodson, S.A.3
-
53
-
-
0032539561
-
Molecular picture of folding of a small alpha/beta protein
-
Sheinerman FB, Brooks III CL (1998) Molecular picture of folding of a small alpha/beta protein, Proc Natl Acad Sci USA, 95: 1562–7
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 1562-1567
-
-
Sheinerman, F.B.1
Brooks, C.L.2
-
54
-
-
0034669844
-
Mechanism of protein folding
-
Nolting B, Andert K (2000) Mechanism of protein folding, Proteins, 41: 288–298
-
(2000)
Proteins
, vol.41
, pp. 288-298
-
-
Nolting, B.1
Andert, K.2
-
55
-
-
0026649261
-
Molecular basis of cooperativity in protein folding. III. Structural identification of cooperative folding units and folding intermediates
-
Murphy KP, Bhakuni V, Xie D, Freire E (1992) Molecular basis of cooperativity in protein folding. III. Structural identification of cooperative folding units and folding intermediates, J Mol Biol, 227: 293–306
-
(1992)
J Mol Biol
, vol.227
, pp. 293-306
-
-
Murphy, K.P.1
Bhakuni, V.2
Xie, D.3
Freire, E.4
-
57
-
-
0031465967
-
New view” of protein folding reconciled with the old through multiple unfolding simulations
-
Lazaridis T, Karplus M (1997) “New view” of protein folding reconciled with the old through multiple unfolding simulations, Science, 278: 1928–1931
-
(1997)
Science
, vol.278
, pp. 1928-1931
-
-
Lazaridis, T.1
Karplus, M.2
-
58
-
-
0036145469
-
Persistently conserved positions in structurally similar, sequence dissimilar proteins: Roles in preserving protein fold and function
-
Friedberg I, Margalit H (2002) Persistently conserved positions in structurally similar, sequence dissimilar proteins: roles in preserving protein fold and function, Protein Sci, 11: 350–360
-
(2002)
Protein Sci
, vol.11
, pp. 350-360
-
-
Friedberg, I.1
Margalit, H.2
-
59
-
-
0034641749
-
Native protein sequences are close to optimal for their structures
-
Kuhlman B, Baker D (2000) Native protein sequences are close to optimal for their structures, Proc Natl Acad Sci USA, 97: 10383–10388
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 10383-10388
-
-
Kuhlman, B.1
Baker, D.2
-
60
-
-
0032744232
-
Protein folding: From the Levinthal paradox to structure prediction
-
Honig B (1999) Protein folding: from the Levinthal paradox to structure prediction, J Mol Biol, 293: 283–293
-
(1999)
J Mol Biol
, vol.293
, pp. 283-293
-
-
Honig, B.1
-
61
-
-
0025370815
-
Dominant forces in protein folding
-
Dill KA (1990) Dominant forces in protein folding, Biochemistry, 29: 7133–55
-
(1990)
Biochemistry
, vol.29
, pp. 7133-7155
-
-
Dill, K.A.1
-
62
-
-
1842298212
-
From Levinthal to pathways to funnels
-
Dill KA and Chan HS (1997) From Levinthal to pathways to funnels, Nat Struct Biol, 4: 10–19
-
(1997)
Nat Struct Biol
, vol.4
, pp. 10-19
-
-
Dill, K.A.1
Chan, H.S.2
-
63
-
-
0035823119
-
Understanding hierarchical protein evolution from first principles
-
Dokholyan NV, Shakhnovich EI (2001) Understanding hierarchical protein evolution from first principles, J Mol Biol, 312: 289–307
-
(2001)
J Mol Biol
, vol.312
, pp. 289-307
-
-
Dokholyan, N.V.1
Shakhnovich, E.I.2
-
64
-
-
0036531903
-
‘Omic’ approaches for unraveling signaling networks
-
Zhu H, Snyder M (2002) ‘Omic’ approaches for unraveling signaling networks, Curr Opin Cell Biol, 14: 173–179
-
(2002)
Curr Opin Cell Biol
, vol.14
, pp. 173-179
-
-
Zhu, H.1
Snyder, M.2
-
65
-
-
0037195144
-
A simple physical model for binding energy hot spots in protein-proteins complexes
-
Kortemme T, Baker D (2002) A simple physical model for binding energy hot spots in protein-proteins complexes, Proc Natl Acad Sci USA, 99: 14116–14121
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 14116-14121
-
-
Kortemme, T.1
Baker, D.2
-
66
-
-
0031058541
-
The statistical-thermodynamic basis for computation of binding affinities: A critical review
-
Gilson MK, Given JA, Bush BL, McCammon JA (1997) The statistical-thermodynamic basis for computation of binding affinities: a critical review, Biophys J, 72: 1047
-
(1997)
Biophys J
, vol.72
, pp. 1047
-
-
Gilson, M.K.1
Given, J.A.2
Bush, B.L.3
McCammon, J.A.4
-
67
-
-
0347949637
-
Revisiting free energy calculations: A theoretical connection to MM/PBSA and direct calculation of the association free energy
-
Swanson JMJ, Henchman RH, McCammon JA (2000) Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy, Biophys J, 86: 67–74
-
(2000)
Biophys J
, vol.86
, pp. 67-74
-
-
Swanson, J.M.J.1
Henchman, R.H.2
McCammon, J.A.3
-
68
-
-
0036286654
-
Free energy simulations come of age: Protein-ligand recognition
-
Simonson T, Archontis G, Karplus M (2002) Free energy simulations come of age: protein-ligand recognition, Acct Chem Res, 35: 430–437
-
(2002)
Acct Chem Res
, vol.35
, pp. 430-437
-
-
Simonson, T.1
Archontis, G.2
Karplus, M.3
-
69
-
-
0034521981
-
Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
-
Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y, Wang W, Donini O, Cieplak P, Srinivasan J, Case DA, Cheatham III TE(2000) Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models, Acc Chem Res, 33: 889–897
-
(2000)
Acc Chem Res
, vol.33
, pp. 889-897
-
-
Kollman, P.A.1
Massova, I.2
Reyes, C.3
Kuhn, B.4
Huo, S.5
Chong, L.6
Lee, M.7
Lee, T.8
Duan, Y.9
Wang, W.10
Donini, O.11
Cieplak, P.12
Srinivasan, J.13
Case, D.A.14
Cheatham, T.E.15
-
71
-
-
33751248238
-
Unravelling Hot Spots – a comprehensive computational mutagenesis study
-
Moreira IS, Fernandes PA, Ramos MJ (2007) Unravelling Hot Spots – a comprehensive computational mutagenesis study, Theor Chem Acc, 117: 99–113
-
(2007)
Theor Chem Acc
, vol.117
, pp. 99-113
-
-
Moreira, I.S.1
Fernandes, P.A.2
Ramos, M.J.3
-
72
-
-
0029794940
-
Quantifying biological specificity: The statistical mechanics of molecular recognition
-
Janin J (1996) Quantifying biological specificity: the statistical mechanics of molecular recognition, Proteins, 25(4): 438–445
-
(1996)
Proteins
, vol.25
, Issue.4
, pp. 438-445
-
-
Janin, J.1
-
73
-
-
0036771626
-
Accelarated Poisson-Boltzmann calculations for static and dynamic systems
-
Luo R, David L, Gilson MK (2002) Accelarated Poisson-Boltzmann calculations for static and dynamic systems, J Comput Chem, 23: 1244–1253
-
(2002)
J Comput Chem
, vol.23
, pp. 1244-1253
-
-
Luo, R.1
David, L.2
Gilson, M.K.3
-
74
-
-
0242696091
-
-
Bjørn Brandsdal O, Österberg F, Almlöf M, Feierberg I, Luzhkov VB, and Åqvist J (2003) Free energy calculations and ligand binding advances in protein chemistry, 66: 123–158
-
(2003)
Free Energy Calculations and Ligand Binding Advances in Protein Chemistry
, vol.66
, pp. 123-158
-
-
Bjørn Brandsdal, O.1
Österberg, F.2
Almlöf, M.3
Feierberg, I.4
Luzhkov, V.B.5
Åqvist, J.6
-
75
-
-
0028454828
-
The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
-
Böhm HJ (1994) The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure, J Comput Aided Mol Des, 8(3), 243–256
-
(1994)
J Comput Aided Mol Des
, vol.8
, Issue.3
, pp. 243-256
-
-
Böhm, H.J.1
-
76
-
-
0031226772
-
Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
-
Eldridge MD, Murray CW, Auton TR, Paolini GV, Mee RP (1997) Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes, J Comput Aided Mol Des, 11: 425–445
-
(1997)
J Comput Aided Mol Des
, vol.11
, pp. 425-445
-
-
Eldridge, M.D.1
Murray, C.W.2
Auton, T.R.3
Paolini, G.V.4
Mee, R.P.5
-
77
-
-
0033137131
-
Prediction of the binding energy for small molecules, peptides and proteins
-
Schapira M, Totrov M, Abagyan R (1999) Prediction of the binding energy for small molecules, peptides and proteins J Mol Recog, 12: 177–190
-
(1999)
J Mol Recog
, vol.12
, pp. 177-190
-
-
Schapira, M.1
Totrov, M.2
Abagyan, R.3
-
78
-
-
0029873155
-
Stability changes upon mutation of solvent-acessible residues in protein evaluated by database-derived potentials
-
Gillis D, Rooman M (1996) Stability changes upon mutation of solvent-acessible residues in protein evaluated by database-derived potentials J Mol Biol, 257: 1112–1126
-
(1996)
J Mol Biol
, vol.257
, pp. 1112-1126
-
-
Gillis, D.1
Rooman, M.2
-
79
-
-
0034645763
-
Knowledge-based scoring function to predict protein-ligand interactions
-
Gohlke H, Hendlich M, Klebe G (2000) Knowledge-based scoring function to predict protein-ligand interactions, J Mol Biol, 295: 337–356
-
(2000)
J Mol Biol
, vol.295
, pp. 337-356
-
-
Gohlke, H.1
Hendlich, M.2
Klebe, G.3
-
80
-
-
0036467249
-
Potential of mean force for protein-protein interaction studies
-
Jiang L, Gao Y, Mao F, Liu Z, Lai L (2002) Potential of mean force for protein-protein interaction studies, Proteins, 46(2): 190–196
-
(2002)
Proteins
, vol.46
, Issue.2
, pp. 190-196
-
-
Jiang, L.1
Gao, Y.2
Mao, F.3
Liu, Z.4
Lai, L.5
-
81
-
-
0033562633
-
Use of pair potentials across protein interfaces in screening predicted docked complexes
-
Moont G, Gabb HA, Stenberg MJ (1999) Use of pair potentials across protein interfaces in screening predicted docked complexes, Proteins, 35: 364
-
(1999)
Proteins
, vol.35
, pp. 364
-
-
Moont, G.1
Gabb, H.A.2
Stenberg, M.J.3
-
82
-
-
0033545622
-
Atomtypes assigned by SMARTS rules. Problems with insufficient data in PDB for some atom types
-
Muegge I, Martin YC (1999) Atomtypes assigned by SMARTS rules. Problems with insufficient data in PDB for some atom types, J Med Chem, 42: 791–804
-
(1999)
J Med Chem
, vol.42
, pp. 791-804
-
-
Muegge, I.1
Martin, Y.C.2
-
83
-
-
0030342727
-
Helmholtz free energies of atom pair interactions in proteins
-
Sippl MJ, Ortner M, Jaritz M, Lackner P, Flockner H (1996) Helmholtz free energies of atom pair interactions in proteins, Fold Des, 1: 289–298
-
(1996)
Fold Des
, vol.1
, pp. 289-298
-
-
Sippl, M.J.1
Ortner, M.2
Jaritz, M.3
Lackner, P.4
Flockner, H.5
-
84
-
-
3242879771
-
Computational alanine scanning of protein-protein interfaces
-
Kortemme T, Kim DE, Baker D (2004) Computational alanine scanning of protein-protein interfaces, SciSTKE, 219: 12–15
-
(2004)
Scistke
, vol.219
, pp. 12-15
-
-
Kortemme, T.1
Kim, D.E.2
Baker, D.3
-
85
-
-
0033367874
-
Rapid empiring scoring functions in virtual screening applications
-
Böhm HJ, Stahl M (1999) Rapid empiring scoring functions in virtual screening applications, Med Chem Res, 9: 445–462
-
(1999)
Med Chem Res
, vol.9
, pp. 445-462
-
-
Böhm, H.J.1
Stahl, M.2
-
87
-
-
0037102958
-
Monte Carlo simulation of the peptide recognition at the consensus binding site of the constant fragment of the human immunoglobulin G: The energy landscape analysis of a hot spot at the intermolecular interface
-
Verkhivker GM, Bouzida D, Gehlhaar DK, Rejto PA, Freer ST, Rose PM (2002) Monte Carlo simulation of the peptide recognition at the consensus binding site of the constant fragment of the human immunoglobulin G: the energy landscape analysis of a hot spot at the intermolecular interface, Proteins, 48: 539–557
-
(2002)
Proteins
, vol.48
, pp. 539-557
-
-
Verkhivker, G.M.1
Bouzida, D.2
Gehlhaar, D.K.3
Rejto, P.A.4
Freer, S.T.5
Rose, P.M.6
-
88
-
-
0031925498
-
Recent advances in structure-based ligand design using molecular mechanics and monte carlo methods
-
Kollman PA (1998) Recent advances in structure-based ligand design using molecular mechanics and monte carlo methods, Pharm Res, 15: 368–370
-
(1998)
Pharm Res
, vol.15
, pp. 368-370
-
-
Kollman, P.A.1
-
89
-
-
0031320150
-
Computational approaches to molecular recognition
-
Lamb ML, Jorgensen WL (1997) Computational approaches to molecular recognition, Curr Opin Chem Biol, 1: 449–457
-
(1997)
Curr Opin Chem Biol
, vol.1
, pp. 449-457
-
-
Lamb, M.L.1
Jorgensen, W.L.2
-
90
-
-
0035665229
-
The linear interaction energy method for predicting ligand binding free energies
-
Åqvist J, Marelius J (2001) The linear interaction energy method for predicting ligand binding free energies, Comb Chem High T Scr, 4: 613–626
-
(2001)
Comb Chem High T Scr
, vol.4
, pp. 613-626
-
-
Åqvist, J.1
Marelius, J.2
-
91
-
-
7044239742
-
Free energy calculations—applications to chemical and biochemical phenomena
-
Kollman PA (1993) Free energy calculations—applications to chemical and biochemical phenomena, Chem Rev, 93: 2395–2317
-
(1993)
Chem Rev
, vol.93
, pp. 2395
-
-
Kollman, P.A.1
-
92
-
-
0037234043
-
Free energy calculations for theophylline binding to an RNA aptamer: Comparison of MM-PBSA and thermodynamic integration methods
-
Gouda H, Kuntz I, Case DA, Kollman PA (2002) Free energy calculations for theophylline binding to an RNA aptamer: comparison of MM-PBSA and thermodynamic integration methods, Biopolymers, 68: 16–34
-
(2002)
Biopolymers
, vol.68
, pp. 16-34
-
-
Gouda, H.1
Kuntz, I.2
Case, D.A.3
Kollman, P.A.4
-
93
-
-
0001692244
-
Lambda dynamics—a new approach to free energy calculations
-
Kong XJ, Brooks III CL (1996) Lambda dynamics—a new approach to free energy calculations, J Chem Phys, 105: 2414–23
-
(1996)
J Chem Phys
, vol.105
, pp. 2414-2423
-
-
Kong, X.J.1
Brooks, C.L.2
-
94
-
-
0009514520
-
New free energy based methods for ligand binding from detailed structure-function to multiple ligand screening
-
NY: Kluwer Academic/Plenum Publishers
-
Banba S, Guo Z, Brooks III CL (2001) New free energy based methods for ligand binding from detailed structure-function to multiple ligand screening, In Free Energy Calculations in Rational Drug Design, NY: Kluwer Academic/Plenum Publishers, 195–223
-
(2001)
Free Energy Calculations in Rational Drug Design
, pp. 195-223
-
-
Banba, S.1
Guo, Z.2
Brooks, C.L.3
-
95
-
-
0033545623
-
Prediction of the binding free energies of new TIBO-like HIV-1 reverse transcriptase using a combination of PROFEC, PB/SA, CMC/MD and free energy calculations
-
Eriksson MAL, Pitera J, Kollman PA (1999) Prediction of the binding free energies of new TIBO-like HIV-1 reverse transcriptase using a combination of PROFEC, PB/SA, CMC/MD and free energy calculations, J Med Chem, 42: 868–881
-
(1999)
J Med Chem
, vol.42
, pp. 868-881
-
-
Eriksson, M.A.L.1
Pitera, J.2
Kollman, P.A.3
-
96
-
-
0035895423
-
Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations, Application to amino acid recognition by aspartyl-tRNA synthetase
-
Archontis G, Simonson T, Karplus M (2001) Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations, Application to amino acid recognition by aspartyl-tRNA synthetase, J Mol Biol, 306(2): 307–327
-
(2001)
J Mol Biol
, vol.306
, Issue.2
, pp. 307-327
-
-
Archontis, G.1
Simonson, T.2
Karplus, M.3
-
97
-
-
33845995126
-
Hot spots computational identification – application to the complex formed between the hen egg-white lysozyme (HEL) and the antibody HyHEL-10
-
Moreira IS, Fernandes PA, Ramos MJ (2006) Hot spots computational identification – application to the complex formed between the hen egg-white lysozyme (HEL) and the antibody HyHEL-10, Int J Quantum Chem, 107: 299–310
-
(2006)
Int J Quantum Chem
, vol.107
, pp. 299-310
-
-
Moreira, I.S.1
Fernandes, P.A.2
Ramos, M.J.3
-
98
-
-
0034213559
-
Conservation of polar residues as hot spots at protein interfaces
-
Hu ZJ, Ma BY, Wolsfon H, Nussinov R (2000) Conservation of polar residues as hot spots at protein interfaces, Proteins, 39(4): 331–342
-
(2000)
Proteins
, vol.39
, Issue.4
, pp. 331-342
-
-
Hu, Z.J.1
Ma, B.Y.2
Wolsfon, H.3
Nussinov, R.4
-
99
-
-
0024362070
-
On the attribution of binding energy in antigen-antibody complexes MCPC 603, D1.3, and HyHEL-5
-
Novotny J, Bruccoleri R, Saul F (1989) On the attribution of binding energy in antigen-antibody complexes MCPC 603, D1.3, and HyHEL-5, Biochemistry, 28: 4735
-
(1989)
Biochemistry
, vol.28
, pp. 4735
-
-
Novotny, J.1
Bruccoleri, R.2
Saul, F.3
-
100
-
-
0025744588
-
Computational method for the design of enzymes with altered substracte specificity
-
Wilso C, Mace J, Agard D (1991) Computational method for the design of enzymes with altered substracte specificity, J Mol Biol, 220: 495
-
(1991)
J Mol Biol
, vol.220
, pp. 495
-
-
Wilso, C.1
Mace, J.2
Agard, D.3
-
101
-
-
0030968991
-
Empirical potentials and functions for protein folding and binding
-
Vadja S, Sippl M, Novotny J (1997) Empirical potentials and functions for protein folding and binding, Curr Opin Struct Biol, 7: 222–228
-
(1997)
Curr Opin Struct Biol
, vol.7
, pp. 222-228
-
-
Vadja, S.1
Sippl, M.2
Novotny, J.3
-
102
-
-
0028347939
-
A simplified amino acid potential for use in structure predictions of proteins
-
Wallqvist A, Uller M (1994) A simplified amino acid potential for use in structure predictions of proteins, Proteins, 18: 267–280
-
(1994)
Proteins
, vol.18
, pp. 267-280
-
-
Wallqvist, A.1
Uller, M.2
-
103
-
-
0031556018
-
Analysis of protein-protein interactions and the effects of amino acid mutations on their energetics. The importance of water molecules in the binding epitope
-
Covell DG, Wallqvist A (1997) Analysis of protein-protein interactions and the effects of amino acid mutations on their energetics. The importance of water molecules in the binding epitope, J Mol Biol, 269: 281–297
-
(1997)
J Mol Biol
, vol.269
, pp. 281-297
-
-
Covell, D.G.1
Wallqvist, A.2
-
104
-
-
0027132431
-
Recognition between a bacterial ribonuclease, barnase, and its natural inhibitor, barstar
-
Guillet V, Laphorn A, Hartley RW, Mauguen Y (1993) Recognition between a bacterial ribonuclease, barnase, and its natural inhibitor, barstar, Structure, 1: 165–177
-
(1993)
Structure
, vol.1
, pp. 165-177
-
-
Guillet, V.1
Laphorn, A.2
Hartley, R.W.3
Mauguen, Y.4
-
105
-
-
0028014642
-
Bound water molecules and conformational stabilization help mediate an antigen-antibody association
-
Bhat TN, Bentley GA, Boulot G, Greene MI, Tello D, Dall’Acqua W, Souchon H, Schwarz FP, Mariuzza RA, Poljak RJ (1994) Bound water molecules and conformational stabilization help mediate an antigen-antibody association, Proc Natl Acad Sci USA, 9: 1089–1093
-
(1994)
Proc Natl Acad Sci USA
, vol.9
, pp. 1089-1093
-
-
Bhat, T.N.1
Bentley, G.A.2
Boulot, G.3
Greene, M.I.4
Tello, D.5
Dall’Acqua, W.6
Souchon, H.7
Schwarz, F.P.8
Mariuzza, R.A.9
Poljak, R.J.10
-
106
-
-
0030598346
-
Crystal structure of an Fv-Fv idiotope-antiidiope complex at 1.9 Å resolution
-
Braden BC, Fields BA, Ysern X, Goldbaum FA, Dall’Acqua W, Schwartz FP, Poljak RJ, Mariuzza RA (1996) Crystal structure of an Fv-Fv idiotope-antiidiope complex at 1.9 Å resolution, J Mol Biol, 264: 137–151
-
(1996)
J Mol Biol
, vol.264
, pp. 137-151
-
-
Braden, B.C.1
Fields, B.A.2
Ysern, X.3
Goldbaum, F.A.4
Dall’Acqua, W.5
Schwartz, F.P.6
Poljak, R.J.7
Mariuzza, R.A.8
-
107
-
-
33751552991
-
Calculating total electrostatic energies with the nonlinear Poisson-Boltzmann equation
-
Sharp K, Honig B (1990) Calculating total electrostatic energies with the nonlinear Poisson-Boltzmann equation, J Phys Chem, 94: 7684–7692
-
(1990)
J Phys Chem
, vol.94
, pp. 7684-7692
-
-
Sharp, K.1
Honig, B.2
-
108
-
-
0025283002
-
Electrostatic interactions in macromolecules: Theory and applications
-
Sharp K, Honig B (1991) Electrostatic interactions in macromolecules: theory and applications, Annu Rev Biophys Chem, 19: 301–332
-
(1991)
Annu Rev Biophys Chem
, vol.19
, pp. 301-332
-
-
Sharp, K.1
Honig, B.2
-
109
-
-
0023155210
-
Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes
-
Ponder J, Richards F (1987) Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes, J Mol Biol, 193: 775
-
(1987)
J Mol Biol
, vol.193
, pp. 775
-
-
Ponder, J.1
Richards, F.2
-
110
-
-
0023346161
-
Free energy calculations by computer simulation
-
Bash P, Singh U, Langridge R, Kollman PA (1987) Free energy calculations by computer simulation, Science, 236: 564
-
(1987)
Science
, vol.236
, pp. 564
-
-
Bash, P.1
Singh, U.2
Langridge, R.3
Kollman, P.A.4
-
111
-
-
0024278562
-
Evaluation of the catalytic free energies in genetically modified proteins
-
Warshel A, Sussman F, Hwang J (1998) Evaluation of the catalytic free energies in genetically modified proteins, J Mol Biol, 201: 139
-
(1998)
J Mol Biol
, vol.201
, pp. 139
-
-
Warshel, A.1
Sussman, F.2
Hwang, J.3
-
112
-
-
0037470581
-
An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes
-
Kortemme T, Morozov AV, Baker D (2003) An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes, J Mol Biol, 326: 1239–1259
-
(2003)
J Mol Biol
, vol.326
, pp. 1239-1259
-
-
Kortemme, T.1
Morozov, A.V.2
Baker, D.3
-
114
-
-
33745467541
-
Unravelling the importance of protein-protein interaction: Application of a computational alanine scanning mutagenesis to the study of the IgG1: Streptococcal protein G (c2 Fragment) complex
-
Moreira IS, Fernandes PA, Ramos MJ (2006) Unravelling the importance of protein-protein interaction: application of a computational alanine scanning mutagenesis to the study of the IgG1: streptococcal protein G (c2 Fragment) complex, J Phys Chem B, 110: 10962
-
(2006)
J Phys Chem B
, vol.110
-
-
Moreira, I.S.1
Fernandes, P.A.2
Ramos, M.J.3
-
115
-
-
0028155689
-
A new method for predicting binding affinity in computer-aided drug design
-
Aqvist J, Medina C, Samuelsson JE (1994) A new method for predicting binding affinity in computer-aided drug design, Protein Eng, 7: 385–391
-
(1994)
Protein Eng
, vol.7
, pp. 385-391
-
-
Aqvist, J.1
Medina, C.2
Samuelsson, J.E.3
-
116
-
-
0001382020
-
Calculations of absolute binding free energies for charged ligands and effects of ling-range electrostatic interactions
-
Aqvist J (1996) Calculations of absolute binding free energies for charged ligands and effects of ling-range electrostatic interactions, J Comput Chem, 17: 1587–1597 Proteins, 63: 811
-
(1996)
J Comput Chem
, vol.17
, pp. 1587-1597
-
-
Aqvist, J.1
-
117
-
-
0031637651
-
Ligand binding affinity prediction by linear interaction energy methods
-
Hansson T, Marelius J, Åqvist J (1998) Ligand binding affinity prediction by linear interaction energy methods, J Comput Aided Mol Des, 12: 27–35
-
(1998)
J Comput Aided Mol Des
, vol.12
, pp. 27-35
-
-
Hansson, T.1
Marelius, J.2
Åqvist, J.3
-
118
-
-
0033557303
-
What determines the van der Waals coefficient in the LIE (Linear interaction energy) method to estimate binding free energies using molecular dynamic simulation
-
Wang W, Wang J, Kollman PA (1999) What determines the van der Waals coefficient in the LIE (linear interaction energy) method to estimate binding free energies using molecular dynamic simulation, Proteins, 34: 395–402
-
(1999)
Proteins
, vol.34
, pp. 395-402
-
-
Wang, W.1
Wang, J.2
Kollman, P.A.3
-
119
-
-
0031023843
-
Molecular dynamics simulations of the docking of substituted N5-deazepterins to dihydrofolate reductase
-
Gorse AD, Cready JE (1997) Molecular dynamics simulations of the docking of substituted N5-deazepterins to dihydrofolate reductase, Protein Eng, 10: 23–30
-
(1997)
Protein Eng
, vol.10
, pp. 23-30
-
-
Gorse, A.D.1
Cready, J.E.2
-
120
-
-
0030906731
-
Binding affinities for sulfonamide inhibitors with human thrombin using Monte Carlo simulations with a linear response method
-
Jones-Hertzog DK, Jorgensen WL (1997) Binding affinities for sulfonamide inhibitors with human thrombin using Monte Carlo simulations with a linear response method, J Med Chem, 40:1539–1549
-
(1997)
J Med Chem
, vol.40
, pp. 1539-1549
-
-
Jones-Hertzog, D.K.1
Jorgensen, W.L.2
-
121
-
-
0035105526
-
Computaional modelling of inhibitor binding to human thrombin
-
Ljungberg KB, Marelius J, Musil D, Svensson P, Norden B, Åqvist J (2001) Computaional modelling of inhibitor binding to human thrombin, Eur J Pharm Sci, 12: 441–446
-
(2001)
Eur J Pharm Sci
, vol.12
, pp. 441-446
-
-
Ljungberg, K.B.1
Marelius, J.2
Musil, D.3
Svensson, P.4
Norden, B.5
Åqvist, J.6
-
122
-
-
0033135425
-
Estimation of the binding affinities of FKBP12 inhibitors using a linear response method
-
Lamb ML, Tirado-Rives J, Jorgensen WL (1999) Estimation of the binding affinities of FKBP12 inhibitors using a linear response method, Bioorg Med Chem, 7: 851–860
-
(1999)
Bioorg Med Chem
, vol.7
, pp. 851-860
-
-
Lamb, M.L.1
Tirado-Rives, J.2
Jorgensen, W.L.3
-
123
-
-
0029975720
-
Binding free energy calculations for P450cam-substracte complexes
-
Paulsen MD, Ornstein RL (1996) Binding free energy calculations for P450cam-substracte complexes, Protein Eng, 9: 567–571
-
(1996)
Protein Eng
, vol.9
, pp. 567-571
-
-
Paulsen, M.D.1
Ornstein, R.L.2
-
124
-
-
0342321950
-
Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease
-
Sham YY, Chu ZT, Tao H, Warshel A (1996) Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease, Proteins, 39(4): 393–407
-
(1996)
Proteins
, vol.39
, Issue.4
, pp. 393-407
-
-
Sham, Y.Y.1
Chu, Z.T.2
Tao, H.3
Warshel, A.4
-
125
-
-
33751158897
-
Modeling Solvent in Biomolecular Systems
-
Smith PE, Pettit BM (1994) Modeling Solvent in Biomolecular Systems, J Phys Chem, 98: 9700
-
(1994)
J Phys Chem
, vol.98
, pp. 9700
-
-
Smith, P.E.1
Pettit, B.M.2
-
126
-
-
0033576654
-
Binding constants of neuraminidase inhibitors: An investigation of the linear interaction energy method
-
Wall ID, Leach AR, Salt DW, Ford MG, Essex JW (1999) Binding constants of neuraminidase inhibitors: an investigation of the linear interaction energy method, J Med Chem, 42: 5142–5152
-
(1999)
J Med Chem
, vol.42
, pp. 5142-5152
-
-
Wall, I.D.1
Leach, A.R.2
Salt, D.W.3
Ford, M.G.4
Essex, J.W.5
-
127
-
-
0344778061
-
Semi-analytical treatment of solvation for molecular mechanics and dynamics
-
Still WC, Tempczyk A, Hawley RC, Hendricksen TJ (1990) Semi-analytical treatment of solvation for molecular mechanics and dynamics, J Am Chem Soc, 112: 6189
-
(1990)
J am Chem Soc
, vol.112
, pp. 6189
-
-
Still, W.C.1
Tempczyk, A.2
Hawley, R.C.3
Hendricksen, T.J.4
-
128
-
-
0035950792
-
New linear interaction method for binding affinity calculations using a continuum solvent mode
-
Zhou R, Friesner RA, Ghosh A, Rizzo RC, Jorgensen WL, Levy J (2001) New linear interaction method for binding affinity calculations using a continuum solvent mode, J Phys Chem B, 105: 10388–10397
-
(2001)
J Phys Chem B
, vol.105
, pp. 10388-10397
-
-
Zhou, R.1
Friesner, R.A.2
Ghosh, A.3
Rizzo, R.C.4
Jorgensen, W.L.5
Levy, J.6
-
129
-
-
0034979318
-
Biomolecular simulations: Recent developments in force field, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions
-
Wang W, Donini O, Reyes CM, Kollman PA(2001) Biomolecular simulations: recent developments in force field, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions, A Rev Biophys Biomol Struct, 30: 211–243
-
(2001)
A Rev Biophys Biomol Struct
, vol.30
, pp. 211-243
-
-
Wang, W.1
Donini, O.2
Reyes, C.M.3
Kollman, P.A.4
-
130
-
-
0033568644
-
Computational alanine scanning to probe protein-protein interactions: A novel approach to evaluate binding free energies
-
Massova I, Kollman PA (1999) Computational alanine scanning to probe protein-protein interactions: a novel approach to evaluate binding free energies, J Am Chem Soc, 121: 8133–8143
-
(1999)
J am Chem Soc
, vol.121
, pp. 8133-8143
-
-
Massova, I.1
Kollman, P.A.2
-
131
-
-
0034084991
-
Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding
-
Massova I, Kollman PA (2000) Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding, Perspectives in drug discovery and design, 18: 113–135
-
(2000)
Perspectives in Drug Discovery and Design
, vol.18
, pp. 113-135
-
-
Massova, I.1
Kollman, P.A.2
-
132
-
-
0034811498
-
Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA
-
Wang J, Morin P, Wang W, Kollman PA (2001) Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA, J Am Chem Soc, 123: 5221–5230
-
(2001)
J am Chem Soc
, vol.123
, pp. 5221-5230
-
-
Wang, J.1
Morin, P.2
Wang, W.3
Kollman, P.A.4
-
133
-
-
0034602373
-
Free energy calculations on dimer stability of the HIV protease using molecular dynamics and a continuum solvent model
-
Wang W, Kollman PA (2000) Free energy calculations on dimer stability of the HIV protease using molecular dynamics and a continuum solvent model, J Mol Biol, 303: 567–582
-
(2000)
J Mol Biol
, vol.303
, pp. 567-582
-
-
Wang, W.1
Kollman, P.A.2
-
134
-
-
0034614387
-
Investigating the binding specificity of U1A-RNA by computational mutagenesis
-
Reyes CM, Kollman PA (2000) Investigating the binding specificity of U1A-RNA by computational mutagenesis, J Mol Biol, 295: 1–6
-
(2000)
J Mol Biol
, vol.295
, pp. 1-6
-
-
Reyes, C.M.1
Kollman, P.A.2
-
135
-
-
0037079570
-
Computational alanine scanning of the 1:1 human growth hormone-receptor complex
-
Huo S, Massova I, Kollman PA (2002) Computational alanine scanning of the 1:1 human growth hormone-receptor complex, J Comput Chem, 23: 15–27
-
(2002)
J Comput Chem
, vol.23
, pp. 15-27
-
-
Huo, S.1
Massova, I.2
Kollman, P.A.3
-
136
-
-
0032560959
-
Continuum solvent studies of the stability of the DNA, RNA, and phosphoramidate-DNA helices
-
Srinivasan J, Cheatham T, Cieplak P, Kollman PA, Case DA (1998) Continuum solvent studies of the stability of the DNA, RNA, and phosphoramidate-DNA helices, J Am Chem Soc, 120: 9401–9409
-
(1998)
J am Chem Soc
, vol.120
, pp. 9401-9409
-
-
Srinivasan, J.1
Cheatham, T.2
Cieplak, P.3
Kollman, P.A.4
Case, D.A.5
-
137
-
-
1442300070
-
Free energy simulations and MM-PBSA analyses on the affinity and specificity of steroid binding to antiestradiol antibody
-
Laitinen T, Kankare JA, Perakyla M (2004) Free energy simulations and MM-PBSA analyses on the affinity and specificity of steroid binding to antiestradiol antibody, Proteins, 55(1): 34–43
-
(2004)
Proteins
, vol.55
, Issue.1
, pp. 34-43
-
-
Laitinen, T.1
Kankare, J.A.2
Perakyla, M.3
-
138
-
-
0036286652
-
Long time dynamics of complex systems
-
Elder R, Ghosh A, Cardenas A (2002) Long time dynamics of complex systems, Acc chem Res, 35: 396–403
-
(2002)
Acc Chem Res
, vol.35
, pp. 396-403
-
-
Elder, R.1
Ghosh, A.2
Cardenas, A.3
-
143
-
-
2142813682
-
Computer simulation of molecular dynamics: Methodology, applications and perspectives in chemistry
-
van Gunsteren WF, Berendsen HJC (1990) Computer simulation of molecular dynamics: methodology, applications and perspectives in chemistry, Angew Chem Int Ed, 29: 992
-
(1990)
Angew Chem Int Ed
, vol.29
, pp. 992
-
-
van Gunsteren, W.F.1
Berendsen, H.J.C.2
-
144
-
-
0025048105
-
Molecular Dynamics Simulations in Biology
-
Karplus M, Petsko GA (1990) Molecular Dynamics Simulations in Biology, Nature, 347: 631
-
(1990)
Nature
, vol.347
, pp. 631
-
-
Karplus, M.1
Petsko, G.A.2
-
145
-
-
85073151309
-
Computational Biochemistry and Biophysics
-
Becker OM, MacKerell Jr AD, Roux B, Watanabe M (2001) Computational Biochemistry and Biophysics, NY: Marcel-Dekker, Inc, 512
-
(2001)
NY: Marcel-Dekker, Inc
, vol.512
-
-
Becker, O.M.1
Mackerell, A.D.2
Roux, B.3
Watanabe, M.4
-
146
-
-
3042988525
-
Conformational analysis 130. MM2. A hydrocarbon force field utilizing V1 and V2 torsional terms
-
Allinger NL (1977) Conformational analysis 130. MM2. A hydrocarbon force field utilizing V1 and V2 torsional terms, J Am Chem Soc, 99: 8127–8134
-
(1977)
J am Chem Soc
, vol.99
, pp. 8127-8134
-
-
Allinger, N.L.1
-
147
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization, dynamics calculations
-
Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus MJ (1983) CHARMM: a program for macromolecular energy, minimization, dynamics calculations, J Comput Chem, 4: 187–217
-
(1983)
J Comput Chem
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.J.6
-
148
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins, J Phys Chem B, 102: 3586–3616
-
(1998)
J Phys Chem B
, vol.102
, pp. 3586-3616
-
-
Mackerell, A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack, R.L.4
Evanseck, J.D.5
-
149
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, organic molecules
-
Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz Jr KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA (1995) A second generation force field for the simulation of proteins, nucleic acids, organic molecules, J Am Chem Soc, 117: 5179–5197
-
(1995)
J am Chem Soc
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
151
-
-
0034979318
-
Biomolecular simulations: Recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic, acid noncovalent interactions
-
Wang W, Donin O, Reyes CM, Kollman PA (2001) Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic, acid noncovalent interactions, Annu Rev Biophys Biomol Struct, 30: 211–243
-
(2001)
Annu Rev Biophys Biomol Struct
, vol.30
, pp. 211-243
-
-
Wang, W.1
Donin, O.2
Reyes, C.M.3
Kollman, P.A.4
-
152
-
-
0000843589
-
Performance of the Amber94, Mmff94, and Opls-A a force fields for modeling organic liquids
-
Kaminski G, Jorgensen WL (1996) Performance of the Amber94, Mmff94, and Opls-A a force fields for modeling organic liquids, J Phys Chem, 100: 18010–18013
-
(1996)
J Phys Chem
, vol.100
, pp. 18010-18013
-
-
Kaminski, G.1
Jorgensen, W.L.2
-
154
-
-
0345151816
-
The critical role of force field in property prediction
-
Jónsdóttir SO, Welsh WJ, Rasmunnen K, Klein RA (1999) The critical role of force field in property prediction, New J Chem, 153–163
-
(1999)
New J Chem
, pp. 153-163
-
-
Jónsdóttir, S.O.1
Welsh, W.J.2
Rasmunnen, K.3
Klein, R.A.4
-
155
-
-
0037571112
-
Merck molecular force field. I basis, form, scope, parameterization, and performance of Mmff94
-
Halgren TA (1996) Merck molecular force field. I basis, form, scope, parameterization, and performance of Mmff94, J Comp Chem, 17: 490–519
-
(1996)
J Comp Chem
, vol.17
, pp. 490-519
-
-
Halgren, T.A.1
-
156
-
-
0011134241
-
Merck molecular force field. II. Mmff94 van der Waals and electrostatic parameters for intermolecular interactions
-
Halgren TA (1996) Merck molecular force field. II. Mmff94 van der Waals and electrostatic parameters for intermolecular interactions, J Comp Chem, 17: 520–552
-
(1996)
J Comp Chem
, vol.17
, pp. 520-552
-
-
Halgren, T.A.1
-
157
-
-
0011143599
-
Merck molecular force field. III. Molecular geometries and vibrational frequencies for Mmff94
-
Halgren TA (1996) Merck molecular force field. III. Molecular geometries and vibrational frequencies for Mmff94, J Comp Chem, 17: 553–586
-
(1996)
J Comp Chem
, vol.17
, pp. 553-586
-
-
Halgren, T.A.1
-
158
-
-
0042041206
-
UFF, a rule based full periodic table force field for molecular mechanics and molecular dynamics simulations
-
Rappe AK, Casewit CJ, Colwell KS, Goddard III WA, Skiff WM (1992) UFF, a rule based full periodic table force field for molecular mechanics and molecular dynamics simulations, J Am Chem Soc, 114: 10024
-
(1992)
J am Chem Soc
, vol.114
-
-
Rappe, A.K.1
Casewit, C.J.2
Colwell, K.S.3
Goddard, W.A.4
Skiff, W.M.5
-
160
-
-
0034237485
-
Molecular dynamics simulation of hen egg white lysozyme: A test of the GROMOS96 force field against nuclear magnetic resonance data
-
Stocker U, van Gunsteren WL (2000) Molecular dynamics simulation of hen egg white lysozyme: a test of the GROMOS96 force field against nuclear magnetic resonance data, Proteins: Struct Funct Genet, 40: 145–531
-
(2000)
Proteins: Struct Funct Genet
, vol.40
, pp. 145-531
-
-
Stocker, U.1
van Gunsteren, W.L.2
-
161
-
-
0001600883
-
Derivation of class II force fields. VII. Nonbonded force field parameters for organic compounds
-
Ewig CS, Thacher TS, Hagler AT (1999) Derivation of class II force fields. VII. Nonbonded force field parameters for organic compounds, J Phys Chem B, 103: 6998–7014
-
(1999)
J Phys Chem B
, vol.103
, pp. 6998-7014
-
-
Ewig, C.S.1
Thacher, T.S.2
Hagler, A.T.3
-
162
-
-
0029633167
-
Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution
-
Levitt M, Hirshberg M, Sharon R, Daggett V (1995) Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution, Comput Phys Commun, 91: 215–231
-
(1995)
Comput Phys Commun
, vol.91
, pp. 215-231
-
-
Levitt, M.1
Hirshberg, M.2
Sharon, R.3
Daggett, V.4
-
164
-
-
84986485648
-
A comparison of conformational energies calculated by molecular mechanics (MM2(85), Sybyl 5.1, Sybyl 5.21, ChemX) and semiempirical (AM1 and PM3) methods
-
Gundertofte K, Palm J, Pettersson I Stamvik A (1991) A comparison of conformational energies calculated by molecular mechanics (MM2(85), Sybyl 5.1, Sybyl 5.21, ChemX) and semiempirical (AM1 and PM3) methods, J Comp Chem, 12: 200–208
-
(1991)
J Comp Chem
, vol.12
, pp. 200-208
-
-
Gundertofte, K.1
Palm, J.2
Pettersson, I.3
Stamvik, A.4
-
165
-
-
0000945584
-
Comparison of conformational energies calculated by several molecular mechanics methods
-
Gundertofte K, Liljefors T, Norrby PO, Pattesson I (1996) Comparison of conformational energies calculated by several molecular mechanics methods, J Comp Chem, 17: 429–449
-
(1996)
J Comp Chem
, vol.17
, pp. 429-449
-
-
Gundertofte, K.1
Liljefors, T.2
Norrby, P.O.3
Pattesson, I.4
-
166
-
-
84988074673
-
An appraisal of molecular force fields for the representation of polypeptides
-
Hall D, Pavitt N (1984) An appraisal of molecular force fields for the representation of polypeptides, J Comp Chem, 5: 441–450
-
(1984)
J Comp Chem
, vol.5
, pp. 441-450
-
-
Hall, D.1
Pavitt, N.2
-
167
-
-
0343213055
-
Performance of empirical potentials (AMBER, CFF95, CVFF, CHARMM, OPS, POLTEV), semiemprical quantum chemical methods (AM1, MNDO/M, PM3) and ab initio Hartree-Fock method for interaction of DNA bases: Comparison of nonempirical beyond Hartree-Fock results
-
Hobza P, Kabelac M, Sponer J, Mejzlik P, Vondrasek J (1997) Performance of empirical potentials (AMBER, CFF95, CVFF, CHARMM, OPS, POLTEV), semiemprical quantum chemical methods (AM1, MNDO/M, PM3) and ab initio Hartree-Fock method for interaction of DNA bases: comparison of nonempirical beyond Hartree-Fock results, J Comp Chem, 18: 1136–1150
-
(1997)
J Comp Chem
, vol.18
, pp. 1136-1150
-
-
Hobza, P.1
Kabelac, M.2
Sponer, J.3
Mejzlik, P.4
Vondrasek, J.5
-
168
-
-
0026483331
-
Comparison of protein models minimized by the all-atom and united atom models in the amber force field
-
Kini RM, Evans HJ (1992) Comparison of protein models minimized by the all-atom and united atom models in the amber force field, J Biomol Structure and Dynamics, 10: 265–279
-
(1992)
J Biomol Structure and Dynamics
, vol.10
, pp. 265-279
-
-
Kini, R.M.1
Evans, H.J.2
-
169
-
-
0024822360
-
A comparison of the CHARMM, AMBER, and ECEPP/2 potential for peptides I
-
Roterman IK, Gibson KD, Scheraga HA (1989) A comparison of the CHARMM, AMBER, and ECEPP/2 potential for peptides I, J Biomol Struct Dynamics, 7: 391–419
-
(1989)
J Biomol Struct Dynamics
, vol.7
, pp. 391-419
-
-
Roterman, I.K.1
Gibson, K.D.2
Scheraga, H.A.3
-
170
-
-
0024836024
-
A comparison of the CHARMM, AMBER, ECEPP/2 potential for peptides II
-
Roterman IK, Lambert MH, Gibson KD, Scheraga HA (1989) A comparison of the CHARMM, AMBER, ECEPP/2 potential for peptides II, J Biomol Struct Dynamics, 7: 421–452
-
(1989)
J Biomol Struct Dynamics
, vol.7
, pp. 421-452
-
-
Roterman, I.K.1
Lambert, M.H.2
Gibson, K.D.3
Scheraga, H.A.4
-
171
-
-
0001658242
-
A empirical examination of potential energy minimization using the well-determined structure of the protein crambin
-
Whitlow M, Teeter MM (1986) A empirical examination of potential energy minimization using the well-determined structure of the protein crambin, J Am Chem Soc, 108: 7163–7172
-
(1986)
J am Chem Soc
, vol.108
, pp. 7163-7172
-
-
Whitlow, M.1
Teeter, M.M.2
-
172
-
-
4444351490
-
Empirical force fields for biological macromolecules: Overview and issues
-
Mackerell Jr AD (2004) Empirical force fields for biological macromolecules: overview and issues, J Comput Chem, 25: 1584–1604
-
(2004)
J Comput Chem
, vol.25
, pp. 1584-1604
-
-
Mackerell, A.D.1
-
173
-
-
2942532422
-
Development and testing of a general amber force field
-
Wang J, Wolf R, Caldwell JW, Kollman PA, Case DA (2004) Development and testing of a general amber force field, J Comput Chem, 25: 1157–1174
-
(2004)
J Comput Chem
, vol.25
, pp. 1157-1174
-
-
Wang, J.1
Wolf, R.2
Caldwell, J.W.3
Kollman, P.A.4
Case, D.A.5
-
174
-
-
0034615759
-
Structure of the S15,S18-rRNA complex: Assembly of the 30S ribosome central domain
-
Agalarov SC, Prasad GS, Funke PM, Stout CD, Williamson Jr JR (2000) Structure of the S15,S18-rRNA complex: assembly of the 30S ribosome central domain, Science, 288: 107–112
-
(2000)
Science
, vol.288
, pp. 107-112
-
-
Agalarov, S.C.1
Prasad, G.S.2
Funke, P.M.3
Stout, C.D.4
Williamson, J.R.5
-
175
-
-
0032577020
-
Walden-inversion-enforced transition-state stabilization in a protein tyrosine phosphatase
-
Alhambra C, Wu L, Zhang ZY, Gao JL (1998) Walden-inversion-enforced transition-state stabilization in a protein tyrosine phosphatase, J Am Chem Soc, 120: 3858–3866
-
(1998)
J am Chem Soc
, vol.120
, pp. 3858-3866
-
-
Alhambra, C.1
Wu, L.2
Zhang, Z.Y.3
Gao, J.L.4
-
176
-
-
0032922174
-
A modified version of the Cornell et al force field with improved sugar pucker phases and helical repeat
-
Cheatham TE, Cieplak P, Kollman PA (1999) A modified version of the Cornell et al force field with improved sugar pucker phases and helical repeat, J Biomol Struct, 16: 845–862
-
(1999)
J Biomol Struct
, vol.16
, pp. 845-862
-
-
Cheatham, T.E.1
Cieplak, P.2
Kollman, P.A.3
-
177
-
-
0348244547
-
Allatom empirical force field for nucleic acids. I. Parameter optimization based on small molecule and condensed phase macromolecular target data
-
Foloppe N, Mackerell AD (2000) Allatom empirical force field for nucleic acids. I. Parameter optimization based on small molecule and condensed phase macromolecular target data, J Comp Chem, 21: 86–120
-
(2000)
J Comp Chem
, vol.21
, pp. 86-120
-
-
Foloppe, N.1
Mackerell, A.D.2
-
178
-
-
0032459726
-
Molecular dynamic simulations of environment and sequence dependent DNA conformations: The development of the BMS nucleic acid force field and comparison with experimental results
-
Langley DR (1998) Molecular dynamic simulations of environment and sequence dependent DNA conformations: the development of the BMS nucleic acid force field and comparison with experimental results, J Biomol Struct, 16: 487–509
-
(1998)
J Biomol Struct
, vol.16
, pp. 487-509
-
-
Langley, D.R.1
-
179
-
-
0030834307
-
Molecular Dynamics Simulations of DNA with Protein’s Consistent GROMOS Force Field and the Role of Counterions’ Symmetry
-
Tapia O, Velasquez I (1997) Molecular Dynamics Simulations of DNA with Protein’s Consistent GROMOS Force Field and the Role of Counterions’ Symmetry, J Am Chem Soc, 119: 5934
-
(1997)
J am Chem Soc
, vol.119
, pp. 5934
-
-
Tapia, O.1
Velasquez, I.2
-
180
-
-
0031728523
-
DNA structure and fluctuations sensed from a 1.1ns molecular dynamics trajectory of a fully charged Zif268-DNAcomplex in water
-
Roxstrom G, Velazquez I, Paulino M, Tapia O (1998) DNA structure and fluctuations sensed from a 1.1ns molecular dynamics trajectory of a fully charged Zif268-DNAcomplex in water, J Biomol Struct, 16: 301–312
-
(1998)
J Biomol Struct
, vol.16
, pp. 301-312
-
-
Roxstrom, G.1
Velazquez, I.2
Paulino, M.3
Tapia, O.4
-
181
-
-
33645961739
-
A smooth particle mesh Ewald method
-
Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG (1995) A smooth particle mesh Ewald method, J Chem Phys, 103: 8577–8593
-
(1995)
J Chem Phys
, vol.103
, pp. 8577-8593
-
-
Essmann, U.1
Perera, L.2
Berkowitz, M.L.3
Darden, T.4
Lee, H.5
Pedersen, L.G.6
-
182
-
-
0001534005
-
An iterative PPPM method for simulating Coulombic systems on distributed memory parallel computers
-
Beckers JVL, Lowe CP, DeLee SW (1998) An iterative PPPM method for simulating Coulombic systems on distributed memory parallel computers, Mol Simul, 20: 369–383
-
(1998)
Mol Simul
, vol.20
, pp. 369-383
-
-
Beckers, J.V.L.1
Lowe, C.P.2
Delee, S.W.3
-
183
-
-
0032221749
-
Recent advances in molecular dynamics simulation towards the realistic representation of biomolecules in solution
-
Cheatham TE, Brooks BR (1998) Recent advances in molecular dynamics simulation towards the realistic representation of biomolecules in solution, Theor Chem Acc, 99: 279–288
-
(1998)
Theor Chem Acc
, vol.99
, pp. 279-288
-
-
Cheatham, T.E.1
Brooks, B.R.2
-
184
-
-
0030999097
-
Molecular dynamics simulations of a fluid bilayer of dipalmi-toylphosphatidylcholine at full hydration, constant pressure, and constant temperature
-
Berger O, Edholm O, Jahnig F (1997) Molecular dynamics simulations of a fluid bilayer of dipalmi-toylphosphatidylcholine at full hydration, constant pressure, and constant temperature, Biophys J, 72: 2002–2013
-
(1997)
Biophys J
, vol.72
, pp. 2002-2013
-
-
Berger, O.1
Edholm, O.2
Jahnig, F.3
-
185
-
-
0034028429
-
Molecular dynamics simulation of dipalmitoylphos-phatidylcholine membrane with cholesterol sulphate
-
Smondyrev AM, Berkowitz ML (2000) Molecular dynamics simulation of dipalmitoylphos-phatidylcholine membrane with cholesterol sulphate, Biophys J, 78: 1672–1680
-
(2000)
Biophys J
, vol.78
, pp. 1672-1680
-
-
Smondyrev, A.M.1
Berkowitz, M.L.2
-
186
-
-
0035846402
-
Simulations of phospholipids using a coarse grain model
-
Shelley JC, Shelley MY, Reeder RC, Bandyopadhyay S, Moore PB, Klein ML (2001) Simulations of phospholipids using a coarse grain model, J Phys Chem B, 105: 9785–9792
-
(2001)
J Phys Chem B
, vol.105
, pp. 9785-9792
-
-
Shelley, J.C.1
Shelley, M.Y.2
Reeder, R.C.3
Bandyopadhyay, S.4
Moore, P.B.5
Klein, M.L.6
-
187
-
-
0042193019
-
The mechanism of vesicle fusion as revealed by molecular dynamics simulations
-
Marrink SJ, Mark AE (2003) The mechanism of vesicle fusion as revealed by molecular dynamics simulations, J Am Chem Soc, 125(37): 11144–11145
-
(2003)
J am Chem Soc
, vol.125
, Issue.37
, pp. 11144-11145
-
-
Marrink, S.J.1
Mark, A.E.2
-
188
-
-
0033577284
-
Calculation of the Ramachandran potential of mean force for a disaccharide in aqueous solution
-
Naidoo KJ, Brady JW(1999) Calculation of the Ramachandran potential of mean force for a disaccharide in aqueous solution, J Am Chem Soc, 121: 2244–2252
-
(1999)
J am Chem Soc
, vol.121
, pp. 2244-2252
-
-
Naidoo, K.J.1
Brady, J.W.2
-
190
-
-
0033972258
-
Relative energies of binding for antibody carbohydrate-antigen complexes computed from free-energy simulations
-
Pathiaseril A, Woods RJ (2000) Relative energies of binding for antibody carbohydrate-antigen complexes computed from free-energy simulations, J Am Chem Soc, 122: 331–338
-
(2000)
J am Chem Soc
, vol.122
, pp. 331-338
-
-
Pathiaseril, A.1
Woods, R.J.2
-
191
-
-
0032540692
-
Use of locally enhanced sampling in free energy calculations: Testing and application to the alpha beta anomerization of glucose
-
Simmerling C, Fox T, Kollman PA (1998) Use of locally enhanced sampling in free energy calculations: testing and application to the alpha beta anomerization of glucose, J Am Chem Soc, 120: 5771–5782
-
(1998)
J am Chem Soc
, vol.120
, pp. 5771-5782
-
-
Simmerling, C.1
Fox, T.2
Kollman, P.A.3
-
192
-
-
0042296402
-
OPLS all-atom force field for carbohydrates
-
Dam W, Frontera A, Tirado-Rives J, Jorgensen WL (1997) OPLS all-atom force field for carbohydrates, J Comp Chem, 18: 1955–1970
-
(1997)
J Comp Chem
, vol.18
, pp. 1955-1970
-
-
Dam, W.1
Frontera, A.2
Tirado-Rives, J.3
Jorgensen, W.L.4
-
193
-
-
0001398008
-
How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
-
JM Wang, P Cieplak, PA Kollman PA (2000) How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J Comp Chem, 21: 1049–1074
-
(2000)
J Comp Chem
, vol.21
, pp. 1049-1074
-
-
Wang, J.M.1
Cieplak, P.2
Pa Kollman, P.A.3
-
194
-
-
0029016182
-
Classical electrostatics in biology and chemistry
-
Honig B, Nicholls A (1995) Classical electrostatics in biology and chemistry, Science, 268: 1144–1149
-
(1995)
Science
, vol.268
, pp. 1144-1149
-
-
Honig, B.1
Nicholls, A.2
-
195
-
-
4243463817
-
Electrostatics in biomolecular structure and dynamics
-
Davis ME, Mccammon JA (1990) Electrostatics in biomolecular structure and dynamics, Chem Rev, 90: 500–521
-
(1990)
Chem Rev
, vol.90
, pp. 500-521
-
-
Davis, M.E.1
McCammon, J.A.2
-
196
-
-
84988141840
-
Solving the finite-difference linearized Poisson-Boltzmann equation: A comparison of relaxation and conjugate gradient methods
-
Davis ME, McCammon JA (1991) Solving the finite-difference linearized Poisson-Boltzmann equation: a comparison of relaxation and conjugate gradient methods, J Comp Chem, 10: 386
-
(1991)
J Comp Chem
, vol.10
, pp. 386
-
-
Davis, M.E.1
McCammon, J.A.2
-
197
-
-
85073169912
-
-
NY: John Wiley & Sons, Inc
-
Bourne P, Weissig H, eds (2003) Structural Bioinformatics, Other Structure-Based Databases, NY: John Wiley & Sons, Inc, 427
-
(2003)
Structural Bioinformatics, Other Structure-Based Databases
, pp. 427
-
-
Bourne, P.1
Weissig, H.2
-
198
-
-
0032968133
-
Implicit solvent models
-
Roux B, Simonson T (1999) Implicit solvent models, Biophys Chem, 78: 1–20
-
(1999)
Biophys Chem
, vol.78
, pp. 1-20
-
-
Roux, B.1
Simonson, T.2
-
199
-
-
14244273182
-
Theory and applications of the generalized Born solvation model in macromolecular simulations
-
Tsui V, Case DA (2001) Theory and applications of the generalized Born solvation model in macromolecular simulations, Biopolymers, 56: 275–291
-
(2001)
Biopolymers
, vol.56
, pp. 275-291
-
-
Tsui, V.1
Case, D.A.2
-
200
-
-
24344502228
-
Accuracy of the numerical differentiation of the Poisson-Boltzmann equation
-
Moreira IS, Fernandes PA and Ramos MJ (2005) Accuracy of the numerical differentiation of the Poisson-Boltzmann equation, J Mol Struct (Theochem), 729: 11–18
-
(2005)
J Mol Struct (Theochem)
, vol.729
, pp. 11-18
-
-
Moreira, I.S.1
Fernandes, P.A.2
Ramos, M.J.3
-
201
-
-
1842479952
-
Exploring protein native states and large-scale conformational changes with a modified generalized Born model
-
Onufriev A, Bashford D, Case DA (2004) Exploring protein native states and large-scale conformational changes with a modified generalized Born model, Proteins, 55: 383–394
-
(2004)
Proteins
, vol.55
, pp. 383-394
-
-
Onufriev, A.1
Bashford, D.2
Case, D.A.3
-
202
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen WL, Chandrasekhar J, Madura J, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water, J Chem Phys, 79: 926–935
-
(1983)
J Chem Phys
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.3
Impey, R.W.4
Klein, M.L.5
-
203
-
-
0000020246
-
A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions
-
Mahoney MW, Jorgensen WL (2000) A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions, J Chem Phys, 112: 8910–8922
-
(2000)
J Chem Phys
, vol.112
, pp. 8910-8922
-
-
Mahoney, M.W.1
Jorgensen, W.L.2
-
205
-
-
0036234027
-
Comparison of protein solution structures refined by molecular dynamics simulations in vacuum, with a generalized Born model, and with explicit water
-
Xia B, Tsui V, Case DA, Dyson J, Wright PE (2002) Comparison of protein solution structures refined by molecular dynamics simulations in vacuum, with a generalized Born model, and with explicit water, J Biomol NMR, 22: 317–331
-
(2002)
J Biomol NMR
, vol.22
, pp. 317-331
-
-
Xia, B.1
Tsui, V.2
Case, D.A.3
Dyson, J.4
Wright, P.E.5
-
206
-
-
0036217783
-
Long time dynamics of met-enkephalin: Comparison of explicit and implicit solvent models
-
Shen M, Freed KF (2002) Long time dynamics of met-enkephalin: comparison of explicit and implicit solvent models, Biophys J, 82: 1791–1808
-
(2002)
Biophys J
, vol.82
, pp. 1791-1808
-
-
Shen, M.1
Freed, K.F.2
-
207
-
-
0029941154
-
Observation of the A DNA to B DNA transition during unrestrained molecular dynamics in aqueous solution
-
Cheatham III TE, Kollman PA (1996) Observation of the A DNA to B DNA transition during unrestrained molecular dynamics in aqueous solution, J Mol Biol, 259: 434–444
-
(1996)
J Mol Biol
, vol.259
, pp. 434-444
-
-
Cheatham, T.E.1
Kollman, P.A.2
-
208
-
-
0346971105
-
Performance comparison of generalized Born and Poisson methods in the calculation of electrostatic solvation energies for protein structures
-
Feig M, Onufriev A, Lee MS, Im W, Case DA, Brooks III CL (2004) Performance comparison of generalized Born and Poisson methods in the calculation of electrostatic solvation energies for protein structures, J Comput Chem, 25: 265–284
-
(2004)
J Comput Chem
, vol.25
, pp. 265-284
-
-
Feig, M.1
Onufriev, A.2
Lee, M.S.3
Im, W.4
Case, D.A.5
Brooks, C.L.6
-
209
-
-
0035964342
-
Electrostatics of nanosystems: Application to microtubules and the ribosome
-
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA (2001) Electrostatics of nanosystems: application to microtubules and the ribosome, Proc Natl Acad Sci USA, 98: 10037–10041
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 10037-10041
-
-
Baker, N.A.1
Sept, D.2
Joseph, S.3
Holst, M.J.4
McCammon, J.A.5
-
210
-
-
84954235985
-
-
The Poisson-Boltzmann Equation, Hoboken, NJ: John Wiley and Sons, Inc
-
Lipkowitz KB, Larter R, Cundari TR, eds (2003) Reviews in Computational Chemistry, The Poisson-Boltzmann Equation, Hoboken, NJ: John Wiley and Sons, Inc, 147
-
(2003)
Reviews in Computational Chemistry
, pp. 147
-
-
Lipkowitz, K.B.1
Larter, R.2
Cundari, T.R.3
-
211
-
-
1942455284
-
Enhanced ab initio protein folding simulations in Poisson-Boltzmann molecular dynamics with self guiding forces
-
Wen EZ, Hsieh MJ, Kollman PA, Luo R (2004) Enhanced ab initio protein folding simulations in Poisson-Boltzmann molecular dynamics with self guiding forces, J Mol Graph Model, 22: 415–424
-
(2004)
J Mol Graph Model
, vol.22
, pp. 415-424
-
-
Wen, E.Z.1
Hsieh, M.J.2
Kollman, P.A.3
Luo, R.4
-
212
-
-
20644449471
-
Modification of the generalized born model suitable for macromolecules
-
Onufriev A, Bashford D, Case DA (2000) Modification of the generalized born model suitable for macromolecules, J Phys Chem B, 104: 3712
-
(2000)
J Phys Chem B
, vol.104
, pp. 3712
-
-
Onufriev, A.1
Bashford, D.2
Case, D.A.3
-
213
-
-
0141956090
-
Generalized born model with a simple smoothing function
-
Im W, Lee MS, Brooks III CL (2003) Generalized born model with a simple smoothing function, J Comput Chem, 24: 1691
-
(2003)
J Comput Chem
, vol.24
, pp. 1691
-
-
Im, W.1
Lee, M.S.2
Brooks, C.L.3
-
214
-
-
0033654297
-
Generalized born models of macromolecular solvation effects
-
Bashford D, Case DA (2000) Generalized born models of macromolecular solvation effects, Annu Rev Phys Chem, 51: 129–152
-
(2000)
Annu Rev Phys Chem
, vol.51
, pp. 129-152
-
-
Bashford, D.1
Case, D.A.2
-
215
-
-
4444323489
-
Solvation forces on biomolecular structures: A comparison of explicit solvent and Poisson-Boltzmann models
-
Wagoner J, Baker N (2004) Solvation forces on biomolecular structures: a comparison of explicit solvent and Poisson-Boltzmann models, J Comput Chem, 25: 1623–1629
-
(2004)
J Comput Chem
, vol.25
, pp. 1623-1629
-
-
Wagoner, J.1
Baker, N.2
-
216
-
-
0032870608
-
Improving macromolecular electrostatics calculations
-
Nielsen JE, Andersen KV, Honig B, Hooft RW, Klebe G, Vriend G, Wade RC (1999) Improving macromolecular electrostatics calculations, Protein Eng, 12(8): 657–662
-
(1999)
Protein Eng
, vol.12
, Issue.8
, pp. 657-662
-
-
Nielsen, J.E.1
Andersen, K.V.2
Honig, B.3
Hooft, R.W.4
Klebe, G.5
Vriend, G.6
Wade, R.C.7
-
217
-
-
0036873086
-
The Poisson-Boltzmann equation for biomolecular electrostatics: A tool for structural biology
-
Fogolari F, Brigo A, Molinari H (2002) The Poisson-Boltzmann equation for biomolecular electrostatics: a tool for structural biology, J Mol Recognit, 15: 377–392
-
(2002)
J Mol Recognit
, vol.15
, pp. 377-392
-
-
Fogolari, F.1
Brigo, A.2
Molinari, H.3
-
218
-
-
0000555535
-
Sur la constitution de la charge électrique a la surface d’un électrolyte
-
Gouy M (1910) Sur la constitution de la charge électrique a la surface d’un électrolyte, J Phys, 9: 457–468
-
(1910)
J Phys
, vol.9
, pp. 457-468
-
-
Gouy, M.1
-
219
-
-
0000264109
-
Chapman DL (1913) A contribution to the theory of electrocapillarity
-
Chapman DL (1913) A contribution to the theory of electrocapillarity, Phill Mag, 25: 475–481
-
Phill Mag
, vol.25
, pp. 475-481
-
-
-
220
-
-
84986486656
-
Rapid finite difference alogrithm, utililizing successive over-relaxation to solve the Poisson-Boltzman equation
-
Nicholls A, Honig B (1991) Rapid finite difference alogrithm, utililizing successive over-relaxation to solve the Poisson-Boltzman equation, J Comput Chem, 12: 435–445
-
(1991)
J Comput Chem
, vol.12
, pp. 435-445
-
-
Nicholls, A.1
Honig, B.2
-
221
-
-
0026319199
-
Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons
-
Nicholls A, Sharp K, Honig B (1991) Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons, Proteins, 11: 281–296
-
(1991)
Proteins
, vol.11
, pp. 281-296
-
-
Nicholls, A.1
Sharp, K.2
Honig, B.3
-
222
-
-
0029633152
-
Electrostatics and diffusion of molecules in solution: Simulations with the University of Houston Brownian Dynamics Program
-
Madura JD (1995) Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics Program, Comput Phys Commun, 91: 57–95
-
(1995)
Comput Phys Commun
, vol.91
, pp. 57-95
-
-
Madura, J.D.1
-
223
-
-
84962346071
-
Dielectric Relaxation in Proteins: A Continuum Electrostatic Model Incorporating Dielectric Heterogeneity of the Protein and Time-Dependent Charges
-
Höfinger S, Simonson T(2000) Dielectric Relaxation in Proteins: A Continuum Electrostatic Model Incorporating Dielectric Heterogeneity of the Protein and Time-Dependent Charges, J Comput Chem, 22: 290
-
(2000)
J Comput Chem
, vol.22
, pp. 290
-
-
Höfinger, S.1
Simonson, T.2
-
224
-
-
0023779259
-
Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis
-
Gilson MK, Honig B (1988) Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis, Proteins Struct Funct Genet, 4: 7–18
-
(1988)
Proteins Struct Funct Genet
, vol.4
, pp. 7-18
-
-
Gilson, M.K.1
Honig, B.2
-
225
-
-
0023899747
-
Energetics of charge-charge interactions in proteins
-
Gilson MK, Honig B (1988) Energetics of charge-charge interactions in proteins, Proteins Struct Funct Genet, 3: 32–52
-
(1988)
Proteins Struct Funct Genet
, vol.3
, pp. 32-52
-
-
Gilson, M.K.1
Honig, B.2
-
226
-
-
33748593093
-
Improving the continuum dielectric approach to calculating pKas of ionizable groups in proteins
-
Demchuk E, Wade RC (1996) Improving the continuum dielectric approach to calculating pKas of ionizable groups in proteins, J Phys Chem, 100: 17373–17387
-
(1996)
J Phys Chem
, vol.100
, pp. 17373-17387
-
-
Demchuk, E.1
Wade, R.C.2
-
227
-
-
1442330396
-
AGBNP, an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling
-
Gallicchio E, Levy RM (2004) AGBNP, an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling, J Comput Chem, 25: 479–499
-
(2004)
J Comput Chem
, vol.25
, pp. 479-499
-
-
Gallicchio, E.1
Levy, R.M.2
-
228
-
-
0037089017
-
The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel non-polar hydration free energy estimators
-
Gallicchio E, Zhang LY, Levy RM (2002) The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel non-polar hydration free energy estimators, J Comput Chem, 23: 517–529
-
(2002)
J Comput Chem
, vol.23
, pp. 517-529
-
-
Gallicchio, E.1
Zhang, L.Y.2
Levy, R.M.3
-
229
-
-
0038509965
-
A novel approach for designing simple point charge models for liquid water with three interaction sites
-
Glattli A, Daura X, van Gunsteren WF (2003) A novel approach for designing simple point charge models for liquid water with three interaction sites, J Comput Chem, 24: 1087–1096
-
(2003)
J Comput Chem
, vol.24
, pp. 1087-1096
-
-
Glattli, A.1
Daura, X.2
van Gunsteren, W.F.3
-
230
-
-
0025290527
-
The structure and function of the aspartic proteinases
-
Davies DR (1990) The structure and function of the aspartic proteinases, Annu Rev Biophys Chem, 19: 189–215
-
(1990)
Annu Rev Biophys Chem
, vol.19
, pp. 189-215
-
-
Davies, D.R.1
-
231
-
-
0031187388
-
Langevin dipoles model for Ab initio calculations of chemical processes in solution: Parametrization and application to hydration free energies of neutral and ionic solutes, and conformational analysis in aqueous solution
-
Florian J, Warshel A (1997) Langevin dipoles model for Ab initio calculations of chemical processes in solution: parametrization and application to hydration free energies of neutral and ionic solutes, and conformational analysis in aqueous solution, J Phys Chem B, 101: 5583–5595
-
(1997)
J Phys Chem B
, vol.101
, pp. 5583-5595
-
-
Florian, J.1
Warshel, A.2
-
232
-
-
0000043930
-
Solvation free energy of biomacromolecules: Parameters for a modified generalized born model consistent with the AMBER force field
-
Jayaram B, Sprous D, Beveridge DL (1998) Solvation free energy of biomacromolecules: parameters for a modified generalized born model consistent with the AMBER force field, J Phys Chem B, 102: 9571–9576
-
(1998)
J Phys Chem B
, vol.102
, pp. 9571-9576
-
-
Jayaram, B.1
Sprous, D.2
Beveridge, D.L.3
-
234
-
-
0031167555
-
Atomic Born radii for continuum electrostatic calculations based on molecular dynamics free energy simulations
-
Nina M, Beglov D, Roux B (1997) Atomic Born radii for continuum electrostatic calculations based on molecular dynamics free energy simulations, J Phys Chem B, 101: 5239–5248
-
(1997)
J Phys Chem B
, vol.101
, pp. 5239-5248
-
-
Nina, M.1
Beglov, D.2
Roux, B.3
-
235
-
-
0027080909
-
Atomic solvation parameters applied to molecular dynamics of proteins in solution
-
Wesson L, Eisenberg D (1992) Atomic solvation parameters applied to molecular dynamics of proteins in solution, Protein Sci, 1: 227–235
-
(1992)
Protein Sci
, vol.1
, pp. 227-235
-
-
Wesson, L.1
Eisenberg, D.2
-
236
-
-
0033003955
-
ES/IS: Estimation of conformational free energy by combining dynamic simulations with explicit solvent with an implicit solvent continuum model
-
Vorobjec YN, Hermans J (1990) ES/IS: estimation of conformational free energy by combining dynamic simulations with explicit solvent with an implicit solvent continuum model, Biophys Chem, 78: 195–205
-
(1990)
Biophys Chem
, vol.78
, pp. 195-205
-
-
Vorobjec, Y.N.1
Hermans, J.2
-
237
-
-
0031022887
-
Additivity principles in biochemistry
-
Dill KA (1997) Additivity principles in biochemistry, J Biol Chem, 272: 701–704
-
(1997)
J Biol Chem
, vol.272
, pp. 701-704
-
-
Dill, K.A.1
-
240
-
-
0000885331
-
Harmonic analysis of large sytems. I methodology
-
Brooks BR, Janezic D, Karplus M (1995) Harmonic analysis of large sytems. I methodology, J Comput Chem, 16: 1522–1542
-
(1995)
J Comput Chem
, vol.16
, pp. 1522-1542
-
-
Brooks, B.R.1
Janezic, D.2
Karplus, M.3
-
241
-
-
84986469420
-
Harmonic analysis of large system. II. Comparison of different protein models
-
Janezic D, Brooks BR (1995) Harmonic analysis of large system. II. Comparison of different protein models, J Comput Chem, 16: 1543–1553
-
(1995)
J Comput Chem
, vol.16
, pp. 1543-1553
-
-
Janezic, D.1
Brooks, B.R.2
-
242
-
-
84986473952
-
Harmonic analysis of large system. III. Comparison with molecular dynamics
-
Janezic D, Venable RM, Brooks BR (1995) Harmonic analysis of large system. III. Comparison with molecular dynamics, J Comput Chem, 16: 1554–1566
-
(1995)
J Comput Chem
, vol.16
, pp. 1554-1566
-
-
Janezic, D.1
Venable, R.M.2
Brooks, B.R.3
-
243
-
-
0001306666
-
Application of the quasi-Gaussian entropy theory to molecular dynamic simulation of Lennard-jones fluids
-
Roccatano D, Amadei A, Apol MEF, Nola AD, Berendsen HJC (1998) Application of the quasi-Gaussian entropy theory to molecular dynamic simulation of Lennard-jones fluids, J Chem Phys, 109: 6358–6363
-
(1998)
J Chem Phys
, vol.109
, pp. 6358-6363
-
-
Roccatano, D.1
Amadei, A.2
Apol, M.E.F.3
Nola, A.D.4
Berendsen, H.J.C.5
-
244
-
-
84961980685
-
Binding of a diverse set of ligands to avidin and streptavidin: An accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models
-
Kuhn B, Kollman PA (2000) Binding of a diverse set of ligands to avidin and streptavidin: an accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models, J Med Chem, 43(20): 3786–3791
-
(2000)
J Med Chem
, vol.43
, Issue.20
, pp. 3786-3791
-
-
Kuhn, B.1
Kollman, P.A.2
-
245
-
-
0037080244
-
Rapid grid-based construction of the molecular surface for both molecules and geometric objects: Applications to the finite difference Poisson-Boltzmann method
-
Rocchia W, Sridharan S, Nicholls A, Alexov E, Chiabrera A, Honig B (2002) Rapid grid-based construction of the molecular surface for both molecules and geometric objects: applications to the finite difference Poisson-Boltzmann method, J Comp Chem, 23: 128–137
-
(2002)
J Comp Chem
, vol.23
, pp. 128-137
-
-
Rocchia, W.1
Sridharan, S.2
Nicholls, A.3
Alexov, E.4
Chiabrera, A.5
Honig, B.6
-
246
-
-
0035913537
-
Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalent ions
-
Rocchia W, Alexov E, Honig B (2001) Extending the applicability of the nonlinear Poisson-Boltzmann equation: multiple dielectric constants and multivalent ions, J Phys Chem B, 105: 6507–6514
-
(2001)
J Phys Chem B
, vol.105
, pp. 6507-6514
-
-
Rocchia, W.1
Alexov, E.2
Honig, B.3
-
247
-
-
0000538815
-
Analytical molecular surface calculation
-
Connolly ML (1983) Analytical molecular surface calculation, J Appl Cryst, 16: 548–558
-
(1983)
J Appl Cryst
, vol.16
, pp. 548-558
-
-
Connolly, M.L.1
-
248
-
-
20444377245
-
Validation and use of the MM-PBSA approach for drug discovery
-
Kuhn B, Gerber P, Schulz-Gasch T, Stahl M (2005) Validation and use of the MM-PBSA approach for drug discovery, J Med Chem, 48: 4040–4048
-
(2005)
J Med Chem
, vol.48
, pp. 4040-4048
-
-
Kuhn, B.1
Gerber, P.2
Schulz-Gasch, T.3
Stahl, M.4
-
249
-
-
0033405041
-
Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7
-
Chong LT, Duan Y, Wang L, Massova I, Massova PA (1999) Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7, Proc Natl Acad Sci USA, 96(25): 14330–14335
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, Issue.25
, pp. 14330-14335
-
-
Chong, L.T.1
Duan, Y.2
Wang, L.3
Massova, I.4
Massova, P.A.5
-
250
-
-
0034630957
-
Theoretical studies suggest a new antifolate as a more potent inhibitor of thymidylate synthase
-
Lee TS, Kollman PA (2000) Theoretical studies suggest a new antifolate as a more potent inhibitor of thymidylate synthase, J Am Chem Soc, 122: 4385–93
-
(2000)
J am Chem Soc
, vol.122
, pp. 4385-4393
-
-
Lee, T.S.1
Kollman, P.A.2
-
251
-
-
0034212858
-
Use of MM-PB/SA in estimating the free energies of proteins: Application to native, intermediates, and unfolded villin headpiece
-
Lee MR, Duan Y, Kollman PA (2000) Use of MM-PB/SA in estimating the free energies of proteins: application to native, intermediates, and unfolded villin headpiece, Proteins, 39(4): 309–316
-
(2000)
Proteins
, vol.39
, Issue.4
, pp. 309-316
-
-
Lee, M.R.1
Duan, Y.2
Kollman, P.A.3
-
252
-
-
0347602124
-
Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf
-
Gohlke H, Case DA (2004) Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf, J Comput Chem, 25(2): 238–250
-
(2004)
J Comput Chem
, vol.25
, Issue.2
, pp. 238-250
-
-
Gohlke, H.1
Case, D.A.2
-
253
-
-
0035575790
-
Hierarchy of simulation models in predicting molecular recognition mechanisms from the binding energy landscapes: Structural analysis of the peptide complexes with SH2 domains
-
Verkhivker GM, Bouzida D, Gehlhaar DK, Rejto PA, Schaffer L, Arthurs S, Colson AB, Freer ST, Larson V, Luty BA, Marrone T, Rose PW (2001) Hierarchy of simulation models in predicting molecular recognition mechanisms from the binding energy landscapes: structural analysis of the peptide complexes with SH2 domains, Proteins, 45(4): 456–470
-
(2001)
Proteins
, vol.45
, Issue.4
, pp. 456-470
-
-
Verkhivker, G.M.1
Bouzida, D.2
Gehlhaar, D.K.3
Rejto, P.A.4
Schaffer, L.5
Arthurs, S.6
Colson, A.B.7
Freer, S.T.8
Larson, V.9
Luty, B.A.10
Marrone, T.11
Rose, P.W.12
-
254
-
-
0033670301
-
Deciphering common failures in molecular docking of ligand-protein complexes
-
Verkhivker GM, Bouzida D, Gehlhaar DK, Rejto PA, Arthurs S, Colson AB, Freer ST, Larson V, BA Marrone T, Rose PW (2000) Deciphering common failures in molecular docking of ligand-protein complexes, J Comput Aided Mol Des, 14(8): 731–751
-
(2000)
J Comput Aided Mol Des
, vol.14
, Issue.8
, pp. 731-751
-
-
Verkhivker, G.M.1
Bouzida, D.2
Gehlhaar, D.K.3
Rejto, P.A.4
Arthurs, S.5
Colson, A.B.6
Freer, S.T.7
Larson, V.8
Ba Marrone, T.9
Rose, P.W.10
-
255
-
-
0002133819
-
Computer simulations of ligand-protein binding with ensembles of protein conformations: A Monte Carlo study of HIV-1 protease binding energy landscapes
-
Bouzida D, Gehlhaar DK, Rejto PA, Schaffer L, Arthurs S, Colson AB, Freer ST, Larson V, Luty BA, Rose PW, Verkhivker GM (1999) Computer simulations of ligand-protein binding with ensembles of protein conformations: a Monte Carlo study of HIV-1 protease binding energy landscapes, Int J Quantum Chem, 73: 73–84
-
(1999)
Int J Quantum Chem
, pp. 73-84
-
-
Bouzida, D.1
Gehlhaar, D.K.2
Rejto, P.A.3
Schaffer, L.4
Arthurs, S.5
Colson, A.B.6
Freer, S.T.7
Larson, V.8
Luty, B.A.9
Rose, P.W.10
Verkhivker, G.M.11
-
256
-
-
0001576820
-
Monte Carlo simulations of ligand-protein binding energy landscapes with the weighted histogram analysis method
-
Bouzida D, Rejto PA, Verkhivker GM(1999) Monte Carlo simulations of ligand-protein binding energy landscapes with the weighted histogram analysis method, Int J Quantum Chem, 73: 113–121
-
(1999)
Int J Quantum Chem
, vol.73
, pp. 113-121
-
-
Bouzida, D.1
Rejto, P.A.2
Verkhivker, G.M.3
-
257
-
-
0033226561
-
Towards understanding the mechanisms of molecular recognition by computer simulations of ligand-protein interactions
-
Verkhivker GM, Rejto PA, Bouzida D, Arthurs S, Colson AB, Freer ST, Gehlhaar DK, Larson V, Luty BA, Marrone T, Rose PW (1999) Towards understanding the mechanisms of molecular recognition by computer simulations of ligand-protein interactions, J Mol Recognit, 12(6): 371–389
-
(1999)
J Mol Recognit
, vol.12
, Issue.6
, pp. 371-389
-
-
Verkhivker, G.M.1
Rejto, P.A.2
Bouzida, D.3
Arthurs, S.4
Colson, A.B.5
Freer, S.T.6
Gehlhaar, D.K.7
Larson, V.8
Luty, B.A.9
Marrone, T.10
Rose, P.W.11
-
258
-
-
0021757436
-
A new force field for molecular mechanical simulation of nucleic acid and proteins
-
Weiner SJ, Kollman PA, Case DA, Singh UC, Chio C, Alagona G, Profeta S, Weiner PA (1984) A new force field for molecular mechanical simulation of nucleic acid and proteins, J Am Chem Soc, 106: 765–784
-
(1984)
J am Chem Soc
, vol.106
, pp. 765-784
-
-
Weiner, S.J.1
Kollman, P.A.2
Case, D.A.3
Singh, U.C.4
Chio, C.5
Alagona, G.6
Profeta, S.7
Weiner, P.A.8
-
259
-
-
0001229337
-
Neighbour-list reduction: Optimization for computation of molecular van der Waals and solvent accessible surface areas
-
Weiser J, Weiser AA, Shenkin PS, Still WC (1998) Neighbour-list reduction: optimization for computation of molecular van der Waals and solvent accessible surface areas, J Comput Chem, 19: 797–808
-
(1998)
J Comput Chem
, vol.19
, pp. 797-808
-
-
Weiser, J.1
Weiser, A.A.2
Shenkin, P.S.3
Still, W.C.4
-
260
-
-
0000408363
-
Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO)
-
Weiser J, Shenkin PS, Still WC (1999) Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO), J Comput Chem, 20: 217–230
-
(1999)
J Comput Chem
, vol.20
, pp. 217-230
-
-
Weiser, J.1
Shenkin, P.S.2
Still, W.C.3
-
261
-
-
0000860122
-
Fast, approximate algorithm for detection of solvent-inacessible atoms
-
Weiser J, Shenkin PS, Still WC (1999), Fast, approximate algorithm for detection of solvent-inacessible atoms, J Comput Chem, 20: 586–596
-
(1999)
J Comput Chem
, vol.20
, pp. 586-596
-
-
Weiser, J.1
Shenkin, P.S.2
Still, W.C.3
-
262
-
-
0034701222
-
Molecular dynamic simulations of nucleic acids with a generalized born solvation model
-
Tsui V, Case DA (2002) Molecular dynamic simulations of nucleic acids with a generalized born solvation model, J Am Chem Soc, 122: 2489–2498
-
(2002)
J am Chem Soc
, vol.122
, pp. 2489-2498
-
-
Tsui, V.1
Case, D.A.2
-
263
-
-
4043171970
-
The GB/SA continuum model for solvation: A fast analytical method for the calculation of approximate born radii
-
Qiu D, Shenkin PS, Hollinger FP, Still WC (1997) The GB/SA continuum model for solvation: a fast analytical method for the calculation of approximate born radii, J Phys Chem A, 101: 3005–3014
-
(1997)
J Phys Chem A
, vol.101
, pp. 3005-3014
-
-
Qiu, D.1
Shenkin, P.S.2
Hollinger, F.P.3
Still, W.C.4
-
264
-
-
0344778061
-
Semianalytical treatment of solvation for molecular mechanics and dynamics
-
Still WC, Tempczyk A, Hawley RC, Hendrickson T (1990) Semianalytical treatment of solvation for molecular mechanics and dynamics, J Am Chem Soc, 112: 6127–6129
-
(1990)
J am Chem Soc
, vol.112
, pp. 6127-6129
-
-
Still, W.C.1
Tempczyk, A.2
Hawley, R.C.3
Hendrickson, T.4
-
265
-
-
84986437005
-
MacroModel – an integrated software system for modelling organic and bioorganic molecules using molecular mechanics
-
Mohamadi F, Richards NGJ, Guida WC, Liskamp R, Lipton M, Caufield C, Chang G, Hendrickson T, Still WC (1990) MacroModel – an integrated software system for modelling organic and bioorganic molecules using molecular mechanics, J Comput Chem, 11: 440–467
-
(1990)
J Comput Chem
, vol.11
, pp. 440-467
-
-
Mohamadi, F.1
Richards, N.G.J.2
Guida, W.C.3
Liskamp, R.4
Lipton, M.5
Caufield, C.6
Chang, G.7
Hendrickson, T.8
Still, W.C.9
-
266
-
-
0024578173
-
Free energy via molecular simulations: Application to chemical and biochemical sytems
-
Beveridge DL, Dicapua FM (1989) Free energy via molecular simulations: application to chemical and biochemical sytems, Annu Rev Biopys Chem, 18: 431–492
-
(1989)
Annu Rev Biopys Chem
, vol.18
, pp. 431-492
-
-
Beveridge, D.L.1
Dicapua, F.M.2
-
267
-
-
33646471468
-
Statistical mechanics of fluid mixtures
-
Kirkwood JG (1935) Statistical mechanics of fluid mixtures, J Chem Phys, 3: 300–313
-
(1935)
J Chem Phys
, vol.3
, pp. 300-313
-
-
Kirkwood, J.G.1
-
268
-
-
36849122972
-
High temperature equation of state by a perturbation method. I. nonpolar gases
-
Zwanzig RW (1954) High temperature equation of state by a perturbation method. I. nonpolar gases, J Chem Phys, 22: 1420–1426
-
(1954)
J Chem Phys
, vol.22
, pp. 1420-1426
-
-
Zwanzig, R.W.1
-
269
-
-
16444385400
-
Monte Carlo free energy estimates using non-Boltzmann sampling: Application to the subcritical Lennard-Jones fluid
-
Torrie GM, Valleau JP (1974) Monte Carlo free energy estimates using non-Boltzmann sampling: application to the subcritical Lennard-Jones fluid, Chem Phys Lett, 28: 578–581
-
(1974)
Chem Phys Lett
, vol.28
, pp. 578-581
-
-
Torrie, G.M.1
Valleau, J.P.2
-
270
-
-
0342929614
-
Nonphysical sampling distributions in Monte Carlo free energy estimation: Umbrella sampling
-
Torrie GM, Valleau JP (1977) Nonphysical sampling distributions in Monte Carlo free energy estimation: umbrella sampling, J Comp Phys, 23: 187–199
-
(1977)
J Comp Phys
, vol.23
, pp. 187-199
-
-
Torrie, G.M.1
Valleau, J.P.2
-
271
-
-
0344227487
-
Thermodynamics of cavity formation in water: A molecular dynamics study
-
Postma JPM, Berendsen HJC, Haak JR, Faraday (1982), Thermodynamics of cavity formation in water: a molecular dynamics study, Symp Chem Soc, 17: 55–67
-
(1982)
Symp Chem Soc
, vol.17
, pp. 55-67
-
-
Postma, J.P.M.1
Berendsen, H.J.C.2
Haakfaraday, J.R.3
-
272
-
-
0007836334
-
Dynamics of reactions in polar solvent. Semiclassical trajectory studies of electron-transfer and proton-transfer reactions
-
Warshel A (1982) Dynamics of reactions in polar solvent. Semiclassical trajectory studies of electron-transfer and proton-transfer reactions, J Phys Chem, 86: 2218–2224
-
(1982)
J Phys Chem
, vol.86
, pp. 2218-2224
-
-
Warshel, A.1
-
273
-
-
33947094574
-
Ab initio calculation of the free energy of liquid water
-
Mezei M, Swaminathan S, Beveridge DL (1978) Ab initio calculation of the free energy of liquid water, J Am Chem Soc, 100: 3255–3256
-
(1978)
J am Chem Soc
, vol.100
, pp. 3255-3256
-
-
Mezei, M.1
Swaminathan, S.2
Beveridge, D.L.3
-
274
-
-
0027486356
-
Application of molecular dynamics and free energy perturbation methods to metalloporphyrin-ligand systems II: CO and dioxygen bynding to myoglobin
-
Lopez MA, Kollman PA (1993) Application of molecular dynamics and free energy perturbation methods to metalloporphyrin-ligand systems II: CO and dioxygen bynding to myoglobin, Protein Sci, 2: 1975–1986
-
(1993)
Protein Sci
, vol.2
, pp. 1975-1986
-
-
Lopez, M.A.1
Kollman, P.A.2
-
275
-
-
0027968902
-
Free energy simulations: The meaning of the individual contributions from a component analysis
-
Boresh S, Archontis G, Karplus M (1994) Free energy simulations: the meaning of the individual contributions from a component analysis, Proteins, 20: 25–33
-
(1994)
Proteins
, vol.20
, pp. 25-33
-
-
Boresh, S.1
Archontis, G.2
Karplus, M.3
-
276
-
-
0000381173
-
Efficient and flexible algorithm for free energy calculations using the lambda-dynamics approach
-
Guo Z, Brooks CL, Kong X (1998) Efficient and flexible algorithm for free energy calculations using the lambda-dynamics approach, J Phys Chem B, 102: 2032–36
-
(1998)
J Phys Chem B
, vol.102
, pp. 2032-2036
-
-
Guo, Z.1
Brooks, C.L.2
Kong, X.3
-
277
-
-
0032481614
-
Rapid screening of binding affinities: Application of the lambda-dynamics method to a trypsin-inhibitor system
-
Guo ZY, Brooks CL (1998) Rapid screening of binding affinities: application of the lambda-dynamics method to a trypsin-inhibitor system, J Am Chem Soc, 120: 1920–21
-
(1998)
J am Chem Soc
, vol.120
, pp. 1920-1921
-
-
Guo, Z.Y.1
Brooks, C.L.2
-
278
-
-
0030134642
-
Estimating the relative free energy of different molecular states with respect to a single reference state
-
Liu HY, Mark AE, Van Gunsteren WF (1996) Estimating the relative free energy of different molecular states with respect to a single reference state, J Phys Chem, 100: 9485–94
-
(1996)
J Phys Chem
, vol.100
, pp. 9485-9494
-
-
Liu, H.Y.1
Mark, A.E.2
van Gunsteren, W.F.3
-
279
-
-
0034669841
-
Exhaustive mutagenesis in silico: Multicoordinate free energy calculations on proteins and peptides
-
Pitera JW, Kollman PA (2000) Exhaustive mutagenesis in silico: multicoordinate free energy calculations on proteins and peptides, Proteins, 41: 385–397
-
(2000)
Proteins
, vol.41
, pp. 385-397
-
-
Pitera, J.W.1
Kollman, P.A.2
-
280
-
-
0032486764
-
Designing na optimum guest for a host using multimolecule free energy calculations: Predicting the best ligand for Rebek’s “tennis ball”
-
Pitera J, Kollman PA (1998) Designing na optimum guest for a host using multimolecule free energy calculations: predicting the best ligand for Rebek’s “tennis ball”, J Am Chem Soc, 120: 7557–67
-
(1998)
J am Chem Soc
, vol.120
, pp. 7557-7567
-
-
Pitera, J.1
Kollman, P.A.2
-
281
-
-
0029557441
-
Estimation of binding free energies for HIV protease inhibitors by molecular dynamic simulations
-
Hansson T, Aqvist J (1995) Estimation of binding free energies for HIV protease inhibitors by molecular dynamic simulations, Protein Eng, 8: 1137–1144
-
(1995)
Protein Eng
, vol.8
, pp. 1137-1144
-
-
Hansson, T.1
Aqvist, J.2
-
282
-
-
0032488817
-
Specific amino acid recognition by aspartyl-tRNA synthetase studied by free energy simulation
-
Archontis G, Simonson T, Moras D, Karplus M (1998) Specific amino acid recognition by aspartyl-tRNA synthetase studied by free energy simulation, J Mol Biol, 275: 823–846
-
(1998)
J Mol Biol
, vol.275
, pp. 823-846
-
-
Archontis, G.1
Simonson, T.2
Moras, D.3
Karplus, M.4
-
283
-
-
0024365336
-
Hidden I thermodynamic of mutant proteins: A molecular dynamics analysis
-
Gao J, Kuczer K, Tidor B, Karplus M (1989) Hidden I thermodynamic of mutant proteins: a molecular dynamics analysis, Science, 244: 1069–1072
-
(1989)
Science
, vol.244
, pp. 1069-1072
-
-
Gao, J.1
Kuczer, K.2
Tidor, B.3
Karplus, M.4
-
284
-
-
0020475509
-
Calculation of the electrostatic potential in the active site cleft due to helix dipoles
-
Warwicker J, Watson H (1982) Calculation of the electrostatic potential in the active site cleft due to helix dipoles, J Mol Biol, 571: 671
-
(1982)
J Mol Biol
, vol.571
, pp. 671
-
-
Warwicker, J.1
Watson, H.2
-
285
-
-
0022988144
-
The modelling of the electrostatic interactions in the function of globular proteins
-
Rogers N (1986) The modelling of the electrostatic interactions in the function of globular proteins, Prog Biophys Mol Biol, 48: 37–66
-
(1986)
Prog Biophys Mol Biol
, vol.48
, pp. 37-66
-
-
Rogers, N.1
-
286
-
-
84988087911
-
Calculating electrostatic interactions in bio-molecules: Method an error assessment
-
Gilson M, Honig B (1988) Calculating electrostatic interactions in bio-molecules: method an error assessment, J Comp Chem, 9: 327–335
-
(1988)
J Comp Chem
, vol.9
, pp. 327-335
-
-
Gilson, M.1
Honig, B.2
-
287
-
-
0032789936
-
Electrostatic interactions in the GCN4 leucine zipper: Substantial contributions arise from intramolecular interactions enhanced on binding
-
Hendsch Z, Tidor B (1999) Electrostatic interactions in the GCN4 leucine zipper: substantial contributions arise from intramolecular interactions enhanced on binding, Protein Sci, 8: 1381–1392
-
(1999)
Protein Sci
, vol.8
, pp. 1381-1392
-
-
Hendsch, Z.1
Tidor, B.2
-
288
-
-
0033970625
-
Modelling Implicit reorganization in continuum descriptions of protein-protein interactions
-
Olson M, Reinke LT (2000) Modelling Implicit reorganization in continuum descriptions of protein-protein interactions, Proteins, 38: 115–119
-
(2000)
Proteins
, vol.38
, pp. 115-119
-
-
Olson, M.1
Reinke, L.T.2
-
289
-
-
0032058875
-
The application of three approximate free energy calculations methods to structure based ligand design: Trypsin and its complex with inhibitors
-
Radmer RJ, Kollman PA (1998) The application of three approximate free energy calculations methods to structure based ligand design: trypsin and its complex with inhibitors, J Comput Aided Mol Des, 12: 215–227
-
(1998)
J Comput Aided Mol Des
, vol.12
, pp. 215-227
-
-
Radmer, R.J.1
Kollman, P.A.2
-
290
-
-
0032698313
-
Free energy grids: A practical qualitative application of free energy perturbation to ligand design using the OWFEG method
-
Pearlman DA (1999) Free energy grids: a practical qualitative application of free energy perturbation to ligand design using the OWFEG method, J Med Chem, 42: 4313
-
(1999)
J Med Chem
, vol.42
, pp. 4313
-
-
Pearlman, D.A.1
-
291
-
-
0000695598
-
Free energy from simulations
-
McCammon JA (1991) Free energy from simulations, Curr Opin Struct Biol, 1: 196
-
(1991)
Curr Opin Struct Biol
, vol.1
, pp. 196
-
-
McCammon, J.A.1
-
292
-
-
33751385859
-
Simulated annealing on free energy surfaces by a combined molecular dynamics and monte carlo approach
-
Tidor B (1993) Simulated annealing on free energy surfaces by a combined molecular dynamics and monte carlo approach, J Phys Chem, 97: 1069–1073
-
(1993)
J Phys Chem
, vol.97
, pp. 1069-1073
-
-
Tidor, B.1
-
293
-
-
33751385859
-
Simulated annealing on free energy surfaces by a combined molecular dynamics and Monte-Carlo approach
-
Tidor B (1993) Simulated annealing on free energy surfaces by a combined molecular dynamics and Monte-Carlo approach, J Phys Chem, 97: 1069–73
-
(1993)
J Phys Chem
, vol.97
, pp. 1069-1073
-
-
Tidor, B.1
-
294
-
-
0034226506
-
Are many-body effects important in protein folding
-
Banba S, Guo Z, Brooks III CL (2000) Are many-body effects important in protein folding? J Phys Chem B, 104: 6903
-
(2000)
J Phys Chem B
, vol.104
, pp. 6903
-
-
Banba, S.1
Guo, Z.2
Brooks, C.L.3
-
295
-
-
0034702638
-
Energetic frustration and the nature of the transition state in protein folding
-
Banba S, Brooks CL (2000) Energetic frustration and the nature of the transition state in protein folding, J Chem Phys, 113: 3423–3433
-
(2000)
J Chem Phys
, vol.113
, pp. 3423-3433
-
-
Banba, S.1
Brooks, C.L.2
-
296
-
-
0031556555
-
Simulated annealing on coupled free energy surfaces: Relative solvation energies of small molecules
-
Jarque C, Tidor B (1997) Simulated annealing on coupled free energy surfaces: relative solvation energies of small molecules, J Phys Chem B, 101: 9362–9374
-
(1997)
J Phys Chem B
, vol.101
, pp. 9362-9374
-
-
Jarque, C.1
Tidor, B.2
-
297
-
-
0025916872
-
Functionality maps of binding sites: A multiple copy simultaneous search method
-
Miranker A, Karplus M (1991) Functionality maps of binding sites: a multiple copy simultaneous search method, Proteins: Struct Funct Genet, 11(1): 29–34
-
(1991)
Proteins: Struct Funct Genet
, vol.11
, Issue.1
, pp. 29-34
-
-
Miranker, A.1
Karplus, M.2
-
298
-
-
5244304444
-
Efficient estimation of free energy differences from Monte Carlo data
-
Bennett CH (1976) Efficient estimation of free energy differences from Monte Carlo data, J Comp Phys, 22: 245–268
-
(1976)
J Comp Phys
, vol.22
, pp. 245-268
-
-
Bennett, C.H.1
-
299
-
-
5744249209
-
Generalizing Swendsen-Wang to sampling – arbitrary posterior probabilities
-
Metropolis NA, Rosenbluth AW, Teller AH, Teller E (1953) Generalizing Swendsen-Wang to sampling – arbitrary posterior probabilities, J Chem Phys, 21: 1087
-
(1953)
J Chem Phys
, vol.21
, pp. 1087
-
-
Metropolis, N.A.1
Rosenbluth, A.W.2
Teller, A.H.3
Teller, E.4
-
300
-
-
85050725410
-
Energy profiles for organic reactions in solution
-
Jorgensen WL (1988) Energy profiles for organic reactions in solution, Adv Chem Phys, 70: 469
-
(1988)
Adv Chem Phys
, vol.70
, pp. 469
-
-
Jorgensen, W.L.1
-
301
-
-
33645941402
-
The OPLS potential functions for proteins, Energy minimizations for crystals of cyclic peptides and crambin
-
Jorgensen WL, Tirado-Rives J (1988) The OPLS potential functions for proteins, Energy minimizations for crystals of cyclic peptides and crambin, J Am Chem Soc, 110: 1657
-
(1988)
J am Chem Soc
, vol.110
, pp. 1657
-
-
Jorgensen, W.L.1
Tirado-Rives, J.2
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