-
1
-
-
1042298843
-
Computational design of protein-protein interactions
-
Kortemme T, Baker D. Computational design of protein-protein interactions. Curr Opin Chem Biol 2004; 8: 91-97.
-
(2004)
Curr Opin Chem Biol
, vol.8
, pp. 91-97
-
-
Kortemme, T.1
Baker, D.2
-
2
-
-
34548528158
-
Progress in computational protein design
-
Lippow SM, Tidor B. Progress in computational protein design. Curr Opin Biotechnol 2007; 18: 305-311.
-
(2007)
Curr Opin Biotechnol
, vol.18
, pp. 305-311
-
-
Lippow, S.M.1
Tidor, B.2
-
4
-
-
0345306764
-
Design of a novel globular protein fold with atomic-level accuracy
-
Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker D. Design of a novel globular protein fold with atomic-level accuracy. Science 2003; 302: 1364-1368.
-
(2003)
Science
, vol.302
, pp. 1364-1368
-
-
Kuhlman, B.1
Dantas, G.2
Ireton, G.C.3
Varani, G.4
Stoddard, B.L.5
Baker, D.6
-
5
-
-
78049316762
-
Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase
-
Frushicheva MP, Cao J, Chu ZT, Warshel A. Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase. Proc Natl Acad Sci U S A 2010; 107: 16869-16874.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 16869-16874
-
-
Frushicheva, M.P.1
Cao, J.2
Chu, Z.T.3
Warshel, A.4
-
6
-
-
23944490117
-
Missense meanderings in sequence space: a biophysical view of protein evolution
-
DePristo MA, Weinreich DM, Hartl DL. Missense meanderings in sequence space: a biophysical view of protein evolution. Nat Rev Genet 2005; 6: 678-687.
-
(2005)
Nat Rev Genet
, vol.6
, pp. 678-687
-
-
DePristo, M.A.1
Weinreich, D.M.2
Hartl, D.L.3
-
7
-
-
0000230329
-
Energetics of enzyme catalysis
-
Warshel A. Energetics of enzyme catalysis. Proc Natl Acad Sci U S A 1978; 75: 5250-5254.
-
(1978)
Proc Natl Acad Sci U S A
, vol.75
, pp. 5250-5254
-
-
Warshel, A.1
-
8
-
-
33748633480
-
Electrostatic basis for enzyme catalysis
-
Warshel A, Sharma PK, Kato M, Xiang Y, Liu H, Olsson MH. Electrostatic basis for enzyme catalysis. Chem Rev 2006; 106: 3210-3235.
-
(2006)
Chem Rev
, vol.106
, pp. 3210-3235
-
-
Warshel, A.1
Sharma, P.K.2
Kato, M.3
Xiang, Y.4
Liu, H.5
Olsson, M.H.6
-
9
-
-
34250181697
-
Stability for function trade-offs in the enolase superfamily "catalytic module"
-
Nagatani RA, Gonzalez A, Shoichet BK, Brinen LS, Babbitt PC. Stability for function trade-offs in the enolase superfamily "catalytic module". Biochemistry 2007; 46: 6688-6695.
-
(2007)
Biochemistry
, vol.46
, pp. 6688-6695
-
-
Nagatani, R.A.1
Gonzalez, A.2
Shoichet, B.K.3
Brinen, L.S.4
Babbitt, P.C.5
-
10
-
-
67650287695
-
In the light of directed evolution: pathways of adaptive protein evolution
-
Bloom JD, Arnold FH. In the light of directed evolution: pathways of adaptive protein evolution. Proc Natl Acad Sci U S A 2009; 106( Suppl 1): 9995-10000.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, Issue.SUPPL. 1
, pp. 9995-10000
-
-
Bloom, J.D.1
Arnold, F.H.2
-
11
-
-
53549085133
-
Evolutionary history of a specialized p450 propane monooxygenase
-
Fasan R, Meharenna YT, Snow CD, Poulos TL, Arnold FH. Evolutionary history of a specialized p450 propane monooxygenase. J Mol Biol 2008; 383: 1069-1080.
-
(2008)
J Mol Biol
, vol.383
, pp. 1069-1080
-
-
Fasan, R.1
Meharenna, Y.T.2
Snow, C.D.3
Poulos, T.L.4
Arnold, F.H.5
-
12
-
-
0036295508
-
Evolution of an antibiotic resistance enzyme constrained by stability and activity trade-offs
-
Wang X, Minasov G, Shoichet BK. Evolution of an antibiotic resistance enzyme constrained by stability and activity trade-offs. J Mol Biol 2002; 320: 85-95.
-
(2002)
J Mol Biol
, vol.320
, pp. 85-95
-
-
Wang, X.1
Minasov, G.2
Shoichet, B.K.3
-
13
-
-
74649086461
-
Structural bases for stability-function tradeoffs in antibiotic resistance
-
Thomas VL, McReynolds AC, Shoichet BK. Structural bases for stability-function tradeoffs in antibiotic resistance. J Mol Biol 2010; 396: 47-59.
-
(2010)
J Mol Biol
, vol.396
, pp. 47-59
-
-
Thomas, V.L.1
McReynolds, A.C.2
Shoichet, B.K.3
-
14
-
-
69549116664
-
Pairwise and higher-order correlations among drug-resistance mutations in HIV-1 subtype B protease
-
Haq O, Levy RM, Morozov AV, Andrec M. Pairwise and higher-order correlations among drug-resistance mutations in HIV-1 subtype B protease. BMC Bioinformatics 2009; 10( Suppl 8): S10.
-
(2009)
BMC Bioinformatics
, vol.10
, Issue.SUPPL. 8
-
-
Haq, O.1
Levy, R.M.2
Morozov, A.V.3
Andrec, M.4
-
15
-
-
38349001243
-
Predicting drug-resistant mutations of HIV protease
-
Ishikita H, Warshel A. Predicting drug-resistant mutations of HIV protease. Angew Chem Int Ed Engl 2008; 47: 697-700.
-
(2008)
Angew Chem Int Ed Engl
, vol.47
, pp. 697-700
-
-
Ishikita, H.1
Warshel, A.2
-
16
-
-
33746377894
-
Protein misfolding, functional amyloid, and human disease
-
Chiti F, Dobson CM. Protein misfolding, functional amyloid, and human disease. Annu Rev Biochem 2006; 75: 333-366.
-
(2006)
Annu Rev Biochem
, vol.75
, pp. 333-366
-
-
Chiti, F.1
Dobson, C.M.2
-
18
-
-
0025732376
-
Simulation analysis of the stability mutant R96H of T4 lysozyme
-
Tidor B, Karplus M. Simulation analysis of the stability mutant R96H of T4 lysozyme. Biochemistry 1991; 30: 3217-3228.
-
(1991)
Biochemistry
, vol.30
, pp. 3217-3228
-
-
Tidor, B.1
Karplus, M.2
-
19
-
-
0029929557
-
Free energy calculations of the mutation of Ile96-Ala in barnase: contributions to the difference in stability
-
Sun YC, Veenstra DL, Kollman PA. Free energy calculations of the mutation of Ile96-Ala in barnase: contributions to the difference in stability. Protein Eng 1996; 9: 273-281.
-
(1996)
Protein Eng
, vol.9
, pp. 273-281
-
-
Sun, Y.C.1
Veenstra, D.L.2
Kollman, P.A.3
-
20
-
-
77952786853
-
Protein thermostability calculations using alchemical free energy simulations
-
Seeliger D, de Groot BL. Protein thermostability calculations using alchemical free energy simulations. Biophys J 2010; 98: 2309-2316.
-
(2010)
Biophys J
, vol.98
, pp. 2309-2316
-
-
Seeliger, D.1
de Groot, B.L.2
-
21
-
-
70049115535
-
Four distances between pairs of amino acids provide a precise description of their interaction
-
Cohen M, Potapov V, Schreiber G. Four distances between pairs of amino acids provide a precise description of their interaction. PLoS Comput Biol 2009; 5: e1000470.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Cohen, M.1
Potapov, V.2
Schreiber, G.3
-
22
-
-
0036291145
-
Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations
-
Guerois R, Nielsen JE, Serrano L. Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol 2002; 320: 369-387.
-
(2002)
J Mol Biol
, vol.320
, pp. 369-387
-
-
Guerois, R.1
Nielsen, J.E.2
Serrano, L.3
-
23
-
-
4544334447
-
Large-scale prediction of protein geometry and stability changes for arbitrary single point mutations
-
Bordner AJ, Abagyan RA. Large-scale prediction of protein geometry and stability changes for arbitrary single point mutations. Proteins 2004; 57: 400-413.
-
(2004)
Proteins
, vol.57
, pp. 400-413
-
-
Bordner, A.J.1
Abagyan, R.A.2
-
24
-
-
14144256681
-
Energy functions for protein design: adjustment with protein-protein complex affinities, models for the unfolded state, and negative design of solubility and specificity
-
Pokala N, Handel TM. Energy functions for protein design: adjustment with protein-protein complex affinities, models for the unfolded state, and negative design of solubility and specificity. J Mol Biol 2005; 347: 203-227.
-
(2005)
J Mol Biol
, vol.347
, pp. 203-227
-
-
Pokala, N.1
Handel, T.M.2
-
25
-
-
58149247893
-
Predicting free energy changes using structural ensembles
-
4.
-
Benedix A, Becker CM, de Groot BL, Caflisch A, Bockmann RA. Predicting free energy changes using structural ensembles. Nat Methods 2009; 6: 3, 4.
-
(2009)
Nat Methods
, vol.6
, pp. 3
-
-
Benedix, A.1
Becker, C.M.2
de Groot, B.L.3
Caflisch, A.4
Bockmann, R.A.5
-
26
-
-
36749018607
-
Modeling backbone flexibility improves protein stability estimation
-
Yin S, Ding F, Dokholyan NV. Modeling backbone flexibility improves protein stability estimation. Structure 2007; 15: 1567-1576.
-
(2007)
Structure
, vol.15
, pp. 1567-1576
-
-
Yin, S.1
Ding, F.2
Dokholyan, N.V.3
-
27
-
-
79551470095
-
Role of conformational sampling in computing mutation-induced changes in protein structure and stability
-
Kellogg EH, Leaver-Fay A, Baker D. Role of conformational sampling in computing mutation-induced changes in protein structure and stability. Proteins 2010; 79: 830-838.
-
(2010)
Proteins
, vol.79
, pp. 830-838
-
-
Kellogg, E.H.1
Leaver-Fay, A.2
Baker, D.3
-
28
-
-
0034641749
-
Native protein sequences are close to optimal for their structures
-
Kuhlman B, Baker D. Native protein sequences are close to optimal for their structures. Proc Natl Acad Sci U S A 2000; 97: 10383-10388.
-
(2000)
Proc Natl Acad Sci U S A
, vol.97
, pp. 10383-10388
-
-
Kuhlman, B.1
Baker, D.2
-
29
-
-
74549207309
-
Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details
-
Potapov V, Cohen M, Schreiber G. Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details. Protein Eng Des Sel 2009; 22: 553-560.
-
(2009)
Protein Eng Des Sel
, vol.22
, pp. 553-560
-
-
Potapov, V.1
Cohen, M.2
Schreiber, G.3
-
30
-
-
0028155689
-
A new method for predicting binding affinity in computer-aided drug design
-
Aqvist J, Medina C, Samuelsson JE. A new method for predicting binding affinity in computer-aided drug design. Protein Eng 1994; 7: 385-391.
-
(1994)
Protein Eng
, vol.7
, pp. 385-391
-
-
Aqvist, J.1
Medina, C.2
Samuelsson, J.E.3
-
31
-
-
0001389474
-
An extended linear-response method for determining free-energies of hydration
-
Carlson HA, Jorgensen WL. An extended linear-response method for determining free-energies of hydration. J Phys Chem 1995; 99: 10667-10673.
-
(1995)
J Phys Chem
, vol.99
, pp. 10667-10673
-
-
Carlson, H.A.1
Jorgensen, W.L.2
-
32
-
-
0022004980
-
Electron transfers in chemistry and biology
-
Marcus RA, Sutin N. Electron transfers in chemistry and biology. Biochim Biophys Acta 1985; 811: 265-322.
-
(1985)
Biochim Biophys Acta
, vol.811
, pp. 265-322
-
-
Marcus, R.A.1
Sutin, N.2
-
33
-
-
5544264558
-
Gaussian fluctuation formula for electrostatic free-energy changes in solution
-
Levy RM, Belhadj M, Kitchen DB. Gaussian fluctuation formula for electrostatic free-energy changes in solution. J Chem Phys 1991; 95: 3627-3633.
-
(1991)
J Chem Phys
, vol.95
, pp. 3627-3633
-
-
Levy, R.M.1
Belhadj, M.2
Kitchen, D.B.3
-
35
-
-
0026596911
-
Calculations of antibody antigen Interactions - Microscopic and semimicroscopic evaluation of the free-energies of binding of phosphorylcholine analogs to Mcpc603
-
Lee FS, Chu ZT, Bolger MB, Warshel A. Calculations of antibody antigen Interactions - Microscopic and semimicroscopic evaluation of the free-energies of binding of phosphorylcholine analogs to Mcpc603. Protein Eng 1992; 5: 215-228.
-
(1992)
Protein Eng
, vol.5
, pp. 215-228
-
-
Lee, F.S.1
Chu, Z.T.2
Bolger, M.B.3
Warshel, A.4
-
36
-
-
0029557441
-
Estimation of binding free energies for HIV proteinase inhibitors by molecular dynamics simulations
-
Hansson T, Aqvist J. Estimation of binding free energies for HIV proteinase inhibitors by molecular dynamics simulations. Protein Eng 1995; 8: 1137-1144.
-
(1995)
Protein Eng
, vol.8
, pp. 1137-1144
-
-
Hansson, T.1
Aqvist, J.2
-
37
-
-
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. 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 2000; 39: 393-407.
-
(2000)
Proteins
, vol.39
, pp. 393-407
-
-
Sham, Y.Y.1
Chu, Z.T.2
Tao, H.3
Warshel, A.4
-
38
-
-
33846308839
-
Calculation of the relative binding affinity of enzyme inhibitors using the generalized linear response method
-
Chen X, Tropsha A. Calculation of the relative binding affinity of enzyme inhibitors using the generalized linear response method. J Chem Theory Comput 2006; 2: 1435-1443.
-
(2006)
J Chem Theory Comput
, vol.2
, pp. 1435-1443
-
-
Chen, X.1
Tropsha, A.2
-
39
-
-
0035950792
-
New linear interaction method for binding affinity calculations using a continuum solvent model
-
Zhou RH, Friesner RA, Ghosh A, Rizzo RC, Jorgensen WL, Levy RM. New linear interaction method for binding affinity calculations using a continuum solvent model. J Phys Chem B 2001; 105: 10388-10397.
-
(2001)
J Phys Chem B
, vol.105
, pp. 10388-10397
-
-
Zhou, R.H.1
Friesner, R.A.2
Ghosh, A.3
Rizzo, R.C.4
Jorgensen, W.L.5
Levy, R.M.6
-
40
-
-
33745799052
-
Continuum solvation models in the linear interaction energy method
-
Carlsson J, Ander M, Nervall M, Aqvist J. Continuum solvation models in the linear interaction energy method. J Phys Chem B 2006; 110: 12034-12041.
-
(2006)
J Phys Chem B
, vol.110
, pp. 12034-12041
-
-
Carlsson, J.1
Ander, M.2
Nervall, M.3
Aqvist, J.4
-
41
-
-
34249021392
-
Linear interaction energy (LIE) models for ligand binding in implicit solvent: theory and application to the binding of NNRTIs to HIV-1 reverse transcriptase
-
Su Y, Gallicchio E, Das K, Arnold E, Levy RM. Linear interaction energy (LIE) models for ligand binding in implicit solvent: theory and application to the binding of NNRTIs to HIV-1 reverse transcriptase. J Chem Theory Comput 2007; 3: 256-277.
-
(2007)
J Chem Theory Comput
, vol.3
, pp. 256-277
-
-
Su, Y.1
Gallicchio, E.2
Das, K.3
Arnold, E.4
Levy, R.M.5
-
42
-
-
34247596467
-
Electrostatic contributions to protein stability and folding energy
-
Roca M, Messer B, Warshel A. Electrostatic contributions to protein stability and folding energy. FEBS Lett 2007; 581: 2065-2071.
-
(2007)
FEBS Lett
, vol.581
, pp. 2065-2071
-
-
Roca, M.1
Messer, B.2
Warshel, A.3
-
43
-
-
70349336345
-
Effective approach for calculations of absolute stability of proteins using focused dielectric constants
-
Vicatos S, Roca M, Warshel A. Effective approach for calculations of absolute stability of proteins using focused dielectric constants. Proteins 2009; 77: 670-684.
-
(2009)
Proteins
, vol.77
, pp. 670-684
-
-
Vicatos, S.1
Roca, M.2
Warshel, A.3
-
44
-
-
0034925093
-
Computational analysis of binding of P1 variants to trypsin
-
Brandsdal BO, Aqvist J, Smalas AO. Computational analysis of binding of P1 variants to trypsin. Protein Sci 2001; 10: 1584-1595.
-
(2001)
Protein Sci
, vol.10
, pp. 1584-1595
-
-
Brandsdal, B.O.1
Aqvist, J.2
Smalas, A.O.3
-
45
-
-
33646166928
-
Probing the effect of point mutations at protein-protein interfaces with free energy calculations
-
Almlof M, Aqvist J, Smalas AO, Brandsdal BO. Probing the effect of point mutations at protein-protein interfaces with free energy calculations. Biophys J 2006; 90: 433-442.
-
(2006)
Biophys J
, vol.90
, pp. 433-442
-
-
Almlof, M.1
Aqvist, J.2
Smalas, A.O.3
Brandsdal, B.O.4
-
46
-
-
1842532008
-
A hierarchical approach to all-atom protein loop prediction
-
Jacobson MP, Pincus DL, Rapp CS, Day TJ, Honig B, Shaw DE, Friesner RA. A hierarchical approach to all-atom protein loop prediction. Proteins 2004; 55: 351-367.
-
(2004)
Proteins
, vol.55
, pp. 351-367
-
-
Jacobson, M.P.1
Pincus, D.L.2
Rapp, C.S.3
Day, T.J.4
Honig, B.5
Shaw, D.E.6
Friesner, R.A.7
-
47
-
-
1442330396
-
AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling
-
Gallicchio E, Levy RM. AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling. J Comput Chem 2004; 25: 479-499.
-
(2004)
J Comput Chem
, vol.25
, pp. 479-499
-
-
Gallicchio, E.1
Levy, R.M.2
-
48
-
-
0029912748
-
Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
-
Jorgensen WL, Maxwell DS, Tirado-Rives J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 1996; 118: 11225-11236.
-
(1996)
J Am Chem Soc
, vol.118
, pp. 11225-11236
-
-
Jorgensen, W.L.1
Maxwell, D.S.2
Tirado-Rives, J.3
-
49
-
-
0035913529
-
Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides
-
Kaminski GA, Friesner RA, Tirado-Rives J, Jorgensen WL. Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J Phys Chem B 2001; 105: 6474-6487.
-
(2001)
J Phys Chem B
, vol.105
, pp. 6474-6487
-
-
Kaminski, G.A.1
Friesner, R.A.2
Tirado-Rives, J.3
Jorgensen, W.L.4
-
50
-
-
33644874615
-
ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions
-
Database issue).
-
Kumar MD, Bava KA, Gromiha MM, Prabakaran P, Kitajima K, Uedaira H, Sarai A. ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions. Nucleic Acids Res 2006; 34: D204-206; (Database issue).
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Kumar, M.D.1
Bava, K.A.2
Gromiha, M.M.3
Prabakaran, P.4
Kitajima, K.5
Uedaira, H.6
Sarai, A.7
-
51
-
-
0025877987
-
The crystal structure of staphylococcal nuclease refined at 1.7 A resolution
-
Hynes TR, Fox RO. The crystal structure of staphylococcal nuclease refined at 1.7 A resolution. Proteins 1991; 10: 92-105.
-
(1991)
Proteins
, vol.10
, pp. 92-105
-
-
Hynes, T.R.1
Fox, R.O.2
-
52
-
-
0027133653
-
Crystal structural analysis of mutations in the hydrophobic cores of barnase
-
Buckle AM, Henrick K, Fersht AR. Crystal structural analysis of mutations in the hydrophobic cores of barnase. J Mol Biol 1993; 234: 847-860.
-
(1993)
J Mol Biol
, vol.234
, pp. 847-860
-
-
Buckle, A.M.1
Henrick, K.2
Fersht, A.R.3
-
53
-
-
0000838678
-
Comparative X-ray structures of the major binding protein for the immunosuppressant FK506 (tacrolimus) in unliganded form and in complex with FK506 and rapamycin
-
Wilson KP, Yamashita MM, Sintchak MD, Rotstein SH, Murcko MA, Boger J, Thomson JA, Fitzgibbon MJ, Black JR, Navia MA. Comparative X-ray structures of the major binding protein for the immunosuppressant FK506 (tacrolimus) in unliganded form and in complex with FK506 and rapamycin. Acta Crystallogr D Biol Crystallogr 1995; 51(Pt 4): 511-521.
-
(1995)
Acta Crystallogr D Biol Crystallogr
, vol.51
, Issue.PART 4
, pp. 511-521
-
-
Wilson, K.P.1
Yamashita, M.M.2
Sintchak, M.D.3
Rotstein, S.H.4
Murcko, M.A.5
Boger, J.6
Thomson, J.A.7
Fitzgibbon, M.J.8
Black, J.R.9
Navia, M.A.10
-
54
-
-
0023652256
-
Crystal and molecular structure of the serine proteinase inhibitor CI-2 from barley seeds
-
McPhalen CA, James MN. Crystal and molecular structure of the serine proteinase inhibitor CI-2 from barley seeds. Biochemistry 1987; 26: 261-269.
-
(1987)
Biochemistry
, vol.26
, pp. 261-269
-
-
McPhalen, C.A.1
James, M.N.2
-
55
-
-
0035074166
-
Structures of the B1 domain of protein L from Peptostreptococcus magnus with a tyrosine to tryptophan substitution
-
O'Neill JW, Kim DE, Baker D, Zhang KY. Structures of the B1 domain of protein L from Peptostreptococcus magnus with a tyrosine to tryptophan substitution. Acta Crystallogr D Biol Crystallogr 2001; 57(Pt 4): 480-487.
-
(2001)
Acta Crystallogr D Biol Crystallogr
, vol.57
, Issue.PART 4
, pp. 480-487
-
-
O'Neill, J.W.1
Kim, D.E.2
Baker, D.3
Zhang, K.Y.4
-
56
-
-
0031025991
-
Three-dimensional structure of the tyrosine kinase c-Src
-
Xu W, Harrison SC, Eck MJ. Three-dimensional structure of the tyrosine kinase c-Src. Nature 1997; 385: 595-602.
-
(1997)
Nature
, vol.385
, pp. 595-602
-
-
Xu, W.1
Harrison, S.C.2
Eck, M.J.3
-
57
-
-
0030457933
-
Three-dimensional structures of the amyloid beta peptide (25-35) in membrane-mimicking environment
-
Kohno T, Kobayashi K, Maeda T, Sato K, Takashima A. Three-dimensional structures of the amyloid beta peptide (25-35) in membrane-mimicking environment. Biochemistry 1996; 35: 16094-16104.
-
(1996)
Biochemistry
, vol.35
, pp. 16094-16104
-
-
Kohno, T.1
Kobayashi, K.2
Maeda, T.3
Sato, K.4
Takashima, A.5
-
58
-
-
0030040589
-
Structure of bovine pancreatic trypsin inhibitor at 125 K definition of carboxyl-terminal residues Gly57 and Ala58
-
Parkin S, Rupp B, Hope H. Structure of bovine pancreatic trypsin inhibitor at 125 K definition of carboxyl-terminal residues Gly57 and Ala58. Acta Crystallogr D Biol Crystallogr 1996; 52(Pt 1): 18-29.
-
(1996)
Acta Crystallogr D Biol Crystallogr
, vol.52
, Issue.PART 1
, pp. 18-29
-
-
Parkin, S.1
Rupp, B.2
Hope, H.3
-
59
-
-
0026342025
-
Structure of the calcium-dependent lectin domain from a rat mannose-binding protein determined by MAD phasing
-
Weis WI, Kahn R, Fourme R, Drickamer K, Hendrickson WA. Structure of the calcium-dependent lectin domain from a rat mannose-binding protein determined by MAD phasing. Science 1991; 254: 1608-1615.
-
(1991)
Science
, vol.254
, pp. 1608-1615
-
-
Weis, W.I.1
Kahn, R.2
Fourme, R.3
Drickamer, K.4
Hendrickson, W.A.5
-
60
-
-
0023104358
-
Structure of bacteriophage T4 lysozyme refined at 1.7 A resolution
-
Weaver LH, Matthews BW. Structure of bacteriophage T4 lysozyme refined at 1.7 A resolution. J Mol Biol 1987; 193: 189-199.
-
(1987)
J Mol Biol
, vol.193
, pp. 189-199
-
-
Weaver, L.H.1
Matthews, B.W.2
-
61
-
-
0036310711
-
On the role of the crystal environment in determining protein side-chain conformations
-
Jacobson MP, Friesner RA, Xiang Z, Honig B. On the role of the crystal environment in determining protein side-chain conformations. J Mol Biol 2002; 320: 597-608.
-
(2002)
J Mol Biol
, vol.320
, pp. 597-608
-
-
Jacobson, M.P.1
Friesner, R.A.2
Xiang, Z.3
Honig, B.4
-
62
-
-
47349128896
-
Toward better refinement of comparative models: predicting loops in inexact environments
-
Sellers BD, Zhu K, Zhao S, Friesner RA, Jacobson MP. Toward better refinement of comparative models: predicting loops in inexact environments. Proteins 2008; 72: 959-971.
-
(2008)
Proteins
, vol.72
, pp. 959-971
-
-
Sellers, B.D.1
Zhu, K.2
Zhao, S.3
Friesner, R.A.4
Jacobson, M.P.5
-
64
-
-
33748988479
-
Long loop prediction using the protein local optimization program
-
Zhu K, Pincus DL, Zhao S, Friesner RA. Long loop prediction using the protein local optimization program. Proteins 2006; 65: 438-452.
-
(2006)
Proteins
, vol.65
, pp. 438-452
-
-
Zhu, K.1
Pincus, D.L.2
Zhao, S.3
Friesner, R.A.4
-
65
-
-
36649014061
-
Improved methods for side chain and loop predictions via the protein local optimization program: variable dielectric model for implicitly improving the treatment of polarization effects
-
Zhu K, Shirts MR, Friesner RA. Improved methods for side chain and loop predictions via the protein local optimization program: variable dielectric model for implicitly improving the treatment of polarization effects. J Chem Theory Comput 2007; 3: 2108-2119.
-
(2007)
J Chem Theory Comput
, vol.3
, pp. 2108-2119
-
-
Zhu, K.1
Shirts, M.R.2
Friesner, R.A.3
-
66
-
-
58149157667
-
Prediction of protein loop conformations using the AGBNP implicit solvent model and torsion angle sampling
-
Felts AK, Gallicchio E, Chekmarev D, Paris KA, Friesner RA, Levy RM. Prediction of protein loop conformations using the AGBNP implicit solvent model and torsion angle sampling. J Chem Theory Comput 2008; 4: 855-868.
-
(2008)
J Chem Theory Comput
, vol.4
, pp. 855-868
-
-
Felts, A.K.1
Gallicchio, E.2
Chekmarev, D.3
Paris, K.A.4
Friesner, R.A.5
Levy, R.M.6
-
67
-
-
31544450787
-
Novel procedure for modeling ligand/receptor induced fit effects
-
Sherman W, Day T, Jacobson MP, Friesner RA, Farid R. Novel procedure for modeling ligand/receptor induced fit effects. J Med Chem 2006; 49: 534-553.
-
(2006)
J Med Chem
, vol.49
, pp. 534-553
-
-
Sherman, W.1
Day, T.2
Jacobson, M.P.3
Friesner, R.A.4
Farid, R.5
-
68
-
-
36148938697
-
Multiscale optimization of a truncated Newton minimization algorithm and application to proteins and protein-ligand complexes
-
Zhu K, Shirts MR, Friesner RA, Jacobson MP. Multiscale optimization of a truncated Newton minimization algorithm and application to proteins and protein-ligand complexes. J Chem Theory Comput 2007; 3: 640-648.
-
(2007)
J Chem Theory Comput
, vol.3
, pp. 640-648
-
-
Zhu, K.1
Shirts, M.R.2
Friesner, R.A.3
Jacobson, M.P.4
-
69
-
-
0035838974
-
Extending the accuracy limits of prediction for side-chain conformations
-
Xiang Z, Honig B. Extending the accuracy limits of prediction for side-chain conformations. J Mol Biol 2001; 311: 421-430.
-
(2001)
J Mol Biol
, vol.311
, pp. 421-430
-
-
Xiang, Z.1
Honig, B.2
-
70
-
-
0001138328
-
Algorithm AS 136: a k-means clustering algorithm
-
Hartigan JA, Wong MA. Algorithm AS 136: a k-means clustering algorithm. J Roy Statist Soc Ser C 1979; 28: 100-108.
-
(1979)
J Roy Statist Soc Ser C
, vol.28
, pp. 100-108
-
-
Hartigan, J.A.1
Wong, M.A.2
-
71
-
-
0344778061
-
Semianalytical treatment of solvation for molecular mechanics and dynamics
-
Still WC, Tempczyk A, Hawley RC, Hendrickson T. Semianalytical treatment of solvation for molecular mechanics and dynamics. J Am Chem Soc 1990; 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
-
72
-
-
0042208326
-
On the nonpolar hydration free energy of proteins: surface area and continuum solvent models for the solute-solvent interaction energy
-
Levy RM, Zhang LY, Gallicchio E, Felts AK. On the nonpolar hydration free energy of proteins: surface area and continuum solvent models for the solute-solvent interaction energy. J Am Chem Soc 2003; 125: 9523-9530.
-
(2003)
J Am Chem Soc
, vol.125
, pp. 9523-9530
-
-
Levy, R.M.1
Zhang, L.Y.2
Gallicchio, E.3
Felts, A.K.4
-
73
-
-
1942540516
-
The non-polar solvent potential of mean force for the dimerization of alanine dipeptide: the role of solute-solvent van der Waals interactions
-
Su Y, Gallicchio E. The non-polar solvent potential of mean force for the dimerization of alanine dipeptide: the role of solute-solvent van der Waals interactions. Biophys Chem 2004; 109: 251-260.
-
(2004)
Biophys Chem
, vol.109
, pp. 251-260
-
-
Su, Y.1
Gallicchio, E.2
-
74
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. J Chem Phys 1983; 79: 926-935.
-
(1983)
J Chem Phys
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
75
-
-
0020997912
-
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983; 22: 2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
76
-
-
0015866154
-
Environment and exposure to solvent of protein atoms. Lysozyme and insulin
-
Shrake A, Rupley JA. Environment and exposure to solvent of protein atoms. Lysozyme and insulin. J Mol Biol 1973; 79: 351-371.
-
(1973)
J Mol Biol
, vol.79
, pp. 351-371
-
-
Shrake, A.1
Rupley, J.A.2
-
77
-
-
70349901079
-
Stability effects of mutations and protein evolvability
-
Tokuriki N, Tawfik DS. Stability effects of mutations and protein evolvability. Curr Opin Struct Biol 2009; 19: 596-604.
-
(2009)
Curr Opin Struct Biol
, vol.19
, pp. 596-604
-
-
Tokuriki, N.1
Tawfik, D.S.2
-
78
-
-
36049027813
-
Protein stability imposes limits on organism complexity and speed of molecular evolution
-
Zeldovich KB, Chen P, Shakhnovich EI. Protein stability imposes limits on organism complexity and speed of molecular evolution. Proc Natl Acad Sci U S A 2007; 104: 16152-16157.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 16152-16157
-
-
Zeldovich, K.B.1
Chen, P.2
Shakhnovich, E.I.3
-
79
-
-
23144461249
-
I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure
-
Web Server issue).
-
Capriotti E, Fariselli P, Casadio R. I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure. Nucleic Acids Res 2005; 33: W306-310; (Web Server issue).
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Capriotti, E.1
Fariselli, P.2
Casadio, R.3
|