-
1
-
-
0002770218
-
Protein folding: Theoretical studies of thermodynamics and dynamics
-
T. Creighton. New York: WH Freeman
-
Karplus M., Shakhnovich E. Protein folding: theoretical studies of thermodynamics and dynamics. Creighton T. Protein Folding. 1992;127-195 WH Freeman, New York.
-
(1992)
Protein Folding
, pp. 127-195
-
-
Karplus, M.1
Shakhnovich, E.2
-
2
-
-
0029094346
-
Enthalpic contribution to protein stability: Atom-based calculations and statistical mechanics
-
Lazaridis T., Archontis G., Karplus M. Enthalpic contribution to protein stability: atom-based calculations and statistical mechanics. Adv Protein Chem. 47:1995;231-306.
-
(1995)
Adv Protein Chem
, vol.47
, pp. 231-306
-
-
Lazaridis, T.1
Archontis, G.2
Karplus, M.3
-
3
-
-
0000991642
-
Harmonic dynamics of proteins: Normal modes and fluctuations in bovine pancreatic trypsin inhibitor
-
Brooks B.R., Karplus M. Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor. Proc Natl Acad Sci USA. 80:1983;6571-6575.
-
(1983)
Proc Natl Acad Sci USA
, vol.80
, pp. 6571-6575
-
-
Brooks, B.R.1
Karplus, M.2
-
4
-
-
0023475026
-
Configurational entropy of native proteins
-
Karplus M., Ichiye T., Pettitt B.M. Configurational entropy of native proteins. Biophys J. 52:1987;1083-1085.
-
(1987)
Biophys J
, vol.52
, pp. 1083-1085
-
-
Karplus, M.1
Ichiye, T.2
Pettitt, B.M.3
-
5
-
-
0031872292
-
Discrimination between native and intentionally misfolded conformations of proteins: ES/IS
-
Vorobjev Y.N., Almagro J.C., Hermans J. Discrimination between native and intentionally misfolded conformations of proteins: ES/IS. Proteins. 32:1998;399-413.
-
(1998)
Proteins
, vol.32
, pp. 399-413
-
-
Vorobjev, Y.N.1
Almagro, J.C.2
Hermans, J.3
-
6
-
-
0032530578
-
Clustering of low energy conformations near the native structures of small proteins
-
Shortle D., Simmons K.T., Baker D. Clustering of low energy conformations near the native structures of small proteins. Proc Natl Acad Sci USA. 95:1998;11158-11162.
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 11158-11162
-
-
Shortle, D.1
Simmons, K.T.2
Baker, D.3
-
7
-
-
0029124248
-
Molten globule and protein folding
-
Ptitsyn O.B. Molten globule and protein folding. Adv Protein Chem. 47:1995;83-229.
-
(1995)
Adv Protein Chem
, vol.47
, pp. 83-229
-
-
Ptitsyn, O.B.1
-
8
-
-
0033548540
-
Side-chain conformational disorder in a molten globule: Molecular dynamics simulations of the A-state of human α-lactalbumin
-
Smith L.J., Dobson C.M., van Gunsteren W.F. Side-chain conformational disorder in a molten globule: molecular dynamics simulations of the A-state of human α-lactalbumin. J Mol Biol. 286:1999;1567-1580.
-
(1999)
J Mol Biol
, vol.286
, pp. 1567-1580
-
-
Smith, L.J.1
Dobson, C.M.2
Van Gunsteren, W.F.3
-
9
-
-
0024733407
-
Intermediates and barrier crossing in a random energy model (with applications to protein folding)
-
Bryngelson J.D., Wolynes P.G. Intermediates and barrier crossing in a random energy model (with applications to protein folding). J Phys Chem. 93:1989;6902-6915.
-
(1989)
J Phys Chem
, vol.93
, pp. 6902-6915
-
-
Bryngelson, J.D.1
Wolynes, P.G.2
-
10
-
-
0028270634
-
Kinetics of protein folding: A lattice model study of the requirements for folding to the native state
-
Sali A., Shakhnovich E., Karplus M. Kinetics of protein folding: a lattice model study of the requirements for folding to the native state. J Mol Biol. 235:1994;1614-1636.
-
(1994)
J Mol Biol
, vol.235
, pp. 1614-1636
-
-
Sali, A.1
Shakhnovich, E.2
Karplus, M.3
-
11
-
-
0032558779
-
Unfolded conformations of α-lytic protease are more stable than its native state
-
Sohl J.L., Jaswal S.S., Agard D.A. Unfolded conformations of α-lytic protease are more stable than its native state. Nature. 395:1998;817-819.
-
(1998)
Nature
, vol.395
, pp. 817-819
-
-
Sohl, J.L.1
Jaswal, S.S.2
Agard, D.A.3
-
12
-
-
0030914617
-
Comparison of database potentials and molecular mechanics force fields
-
Moult J. Comparison of database potentials and molecular mechanics force fields. Curr Opin Struct Biol. 7:1997;194-199.
-
(1997)
Curr Opin Struct Biol
, vol.7
, pp. 194-199
-
-
Moult, J.1
-
13
-
-
0031465967
-
'New view' of protein folding reconciled with the old through multiple unfolding simulations
-
Lazaridis T., Karplus M. 'New view' of protein folding reconciled with the old through multiple unfolding simulations. Science. 278:1997;1928-1931.
-
(1997)
Science
, vol.278
, pp. 1928-1931
-
-
Lazaridis, T.1
Karplus, M.2
-
14
-
-
84863091360
-
Locating all transition states and studying the reaction pathways of potential energy surfaces
-
Westerberg K.M., Floudas C.A. Locating all transition states and studying the reaction pathways of potential energy surfaces. J Chem Phys. 110:1999;9259-9295.
-
(1999)
J Chem Phys
, vol.110
, pp. 9259-9295
-
-
Westerberg, K.M.1
Floudas, C.A.2
-
15
-
-
0033610078
-
Global optimization of clusters, crystals, and biomolecules
-
Wales D.J., Scheraga H.A. Global optimization of clusters, crystals, and biomolecules. Science. 285:1999;1368-1372.
-
(1999)
Science
, vol.285
, pp. 1368-1372
-
-
Wales, D.J.1
Scheraga, H.A.2
-
16
-
-
0030904524
-
Novel methods of sampling phase space in the simulation of biological systems
-
Berne B.J., Straub J.E. Novel methods of sampling phase space in the simulation of biological systems. Curr Opin Struct Biol. 7:1997;181-189.
-
(1997)
Curr Opin Struct Biol
, vol.7
, pp. 181-189
-
-
Berne, B.J.1
Straub, J.E.2
-
17
-
-
0001392923
-
Comparing search strategies for finding global optima on energy landscapes
-
Foreman K.W., Phillips A.T., Rosen J.B., Dill K.A. Comparing search strategies for finding global optima on energy landscapes. J Comput Chem. 20:1999;1527-1537.
-
(1999)
J Comput Chem
, vol.20
, pp. 1527-1537
-
-
Foreman, K.W.1
Phillips, A.T.2
Rosen, J.B.3
Dill, K.A.4
-
18
-
-
0026785519
-
Contact potential that recognizes the correct folding of globular proteins
-
Maiorov V.N., Crippen G.M. Contact potential that recognizes the correct folding of globular proteins. J Mol Biol. 227:1992;876-888.
-
(1992)
J Mol Biol
, vol.227
, pp. 876-888
-
-
Maiorov, V.N.1
Crippen, G.M.2
-
19
-
-
0033117762
-
Designing potential energy functions for protein folding
-
Hao M-H., Scheraga H.A. Designing potential energy functions for protein folding. Curr Opin Struct Biol. 9:1999;184-188.
-
(1999)
Curr Opin Struct Biol
, vol.9
, pp. 184-188
-
-
Hao, M.-H.1
Scheraga, H.A.2
-
20
-
-
0032539910
-
Self-consistently optimized energy functions for protein structure prediction by molecular dynamics
-
Koretke K.K., Luthey-Schulten Z., Wolynes P.G. Self-consistently optimized energy functions for protein structure prediction by molecular dynamics. Proc Natl Acad Sci USA. 95:1998;2932-2937.
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 2932-2937
-
-
Koretke, K.K.1
Luthey-Schulten, Z.2
Wolynes, P.G.3
-
21
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell A.D. Jr., Bashford D., Bellott M., Dunbrack R.L. Jr., Evanseck J.D., Field M.J., Fischer S., Gao J., Guo H., Ha S.et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B. 102:1998;3586-3616.
-
(1998)
J Phys Chem B
, vol.102
, pp. 3586-3616
-
-
MacKerell A.D., Jr.1
Bashford, D.2
Bellott, M.3
Dunbrack R.L., Jr.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
-
22
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
-
Brooks B.R., Bruccoleri R.E., Olafson B.D., States D.J., Swaminathan S., Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem. 4:1983;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.6
-
23
-
-
0033135638
-
Effective energy function for proteins in solution
-
Lazaridis T., Karplus M. Effective energy function for proteins in solution. Proteins. 35:1999;133-152.
-
(1999)
Proteins
, vol.35
, pp. 133-152
-
-
Lazaridis, T.1
Karplus, M.2
-
25
-
-
0021691918
-
An analysis of incorrectly folded protein models. Implications for structure predictions
-
Novotny J., Bruccoleri R., Karplus M. An analysis of incorrectly folded protein models. Implications for structure predictions. J Mol Biol. 177:1984;787-818.
-
(1984)
J Mol Biol
, vol.177
, pp. 787-818
-
-
Novotny, J.1
Bruccoleri, R.2
Karplus, M.3
-
26
-
-
0033531959
-
Discrimination of the native from misfolded protein models with an energy function including implicit solvation
-
Lazaridis T., Karplus M. Discrimination of the native from misfolded protein models with an energy function including implicit solvation. J Mol Biol. 288:1999;477-487.
-
(1999)
J Mol Biol
, vol.288
, pp. 477-487
-
-
Lazaridis, T.1
Karplus, M.2
-
28
-
-
0029942661
-
Structure-derived potentials and protein simulations
-
Jernigan R.L., Bahar I. Structure-derived potentials and protein simulations. Curr Opin Struct Biol. 6:1996;195-209.
-
(1996)
Curr Opin Struct Biol
, vol.6
, pp. 195-209
-
-
Jernigan, R.L.1
Bahar, I.2
-
30
-
-
0029000696
-
Knowledge-based potentials for proteins
-
Sippl M.J. Knowledge-based potentials for proteins. Curr Opin Struct Biol. 5:1995;229-235.
-
(1995)
Curr Opin Struct Biol
, vol.5
, pp. 229-235
-
-
Sippl, M.J.1
-
31
-
-
0030968991
-
Empirical potentials and functions for protein folding and binding
-
Vajda S., Sippl M., Novotny J. Empirical potentials and functions for protein folding and binding. Curr Opin Struct Biol. 7:1997;222-228.
-
(1997)
Curr Opin Struct Biol
, vol.7
, pp. 222-228
-
-
Vajda, S.1
Sippl, M.2
Novotny, J.3
-
32
-
-
0027234766
-
Engineering of stable and fast-folding sequences of model proteins
-
Shakhnovich E.I., Gutin A.M. Engineering of stable and fast-folding sequences of model proteins. Proc Natl Acad Sci USA. 90:1993;7195-7199.
-
(1993)
Proc Natl Acad Sci USA
, vol.90
, pp. 7195-7199
-
-
Shakhnovich, E.I.1
Gutin, A.M.2
-
33
-
-
0030596063
-
How to derive a protein folding potential?
-
Mirny L.A., Shakhnovich E.I. How to derive a protein folding potential? J Mol Biol. 264:1996;1164-1179.
-
(1996)
J Mol Biol
, vol.264
, pp. 1164-1179
-
-
Mirny, L.A.1
Shakhnovich, E.I.2
-
34
-
-
0000560203
-
Fluctuating charge, polarizable dipole, and combined models: Parameterization from ab initio quantum chemistry
-
Stern H.A., Kaminski G.A., Banks J.L., Zhou R., Berne B.J., Friesner R.A. Fluctuating charge, polarizable dipole, and combined models: parameterization from ab initio quantum chemistry. J Phys Chem B. 103:1999;4730-4737.
-
(1999)
J Phys Chem B
, vol.103
, pp. 4730-4737
-
-
Stern, H.A.1
Kaminski, G.A.2
Banks, J.L.3
Zhou, R.4
Berne, B.J.5
Friesner, R.A.6
-
35
-
-
0001064488
-
Statistical potentials extracted from protein structures: Are these meaningful potentials?
-
Ben-Naim A. Statistical potentials extracted from protein structures: are these meaningful potentials? J Chem Phys. 107:1997;3698-3706.
-
(1997)
J Chem Phys
, vol.107
, pp. 3698-3706
-
-
Ben-Naim, A.1
-
36
-
-
0029976427
-
Statistical potentials extracted from protein structures: How accurate are they?
-
Thomas P.D., Dill K.A. Statistical potentials extracted from protein structures: how accurate are they? J Mol Biol. 257:1996;457-469.
-
(1996)
J Mol Biol
, vol.257
, pp. 457-469
-
-
Thomas, P.D.1
Dill, K.A.2
-
37
-
-
0031566950
-
Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation
-
Bahar I., Jernigan R.L. Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation. J Mol Biol. 266:1997;195-214.
-
(1997)
J Mol Biol
, vol.266
, pp. 195-214
-
-
Bahar, I.1
Jernigan, R.L.2
-
38
-
-
0000171351
-
Pairwise contact potentials are unsuitable for protein folding
-
Vendruscolo M., Domany E. Pairwise contact potentials are unsuitable for protein folding. J Chem Phys. 109:1998;11101-11108.
-
(1998)
J Chem Phys
, vol.109
, pp. 11101-11108
-
-
Vendruscolo, M.1
Domany, E.2
-
39
-
-
0031585984
-
Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
-
Simons K.T., Kooperberg C., Huang E., Baker D. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol. 268:1997;209-225.
-
(1997)
J Mol Biol
, vol.268
, pp. 209-225
-
-
Simons, K.T.1
Kooperberg, C.2
Huang, E.3
Baker, D.4
-
40
-
-
0032147142
-
Recognition of native structures from complete enumeration of low-resolution models with constraints
-
Ozkan B., Bahar I. Recognition of native structures from complete enumeration of low-resolution models with constraints. Proteins. 32:1998;211-222.
-
(1998)
Proteins
, vol.32
, pp. 211-222
-
-
Ozkan, B.1
Bahar, I.2
-
41
-
-
0029987862
-
Energy functions that discriminate X-ray and near-native folds from well-constructed decoys
-
Park B., Levitt M. Energy functions that discriminate X-ray and near-native folds from well-constructed decoys. J Mol Biol. 258:1996;367-392.
-
(1996)
J Mol Biol
, vol.258
, pp. 367-392
-
-
Park, B.1
Levitt, M.2
-
42
-
-
0033104694
-
Characterization of internal motions of E. coli ribonuclease H by Monte Carlo simulations
-
Haliloglu T. Characterization of internal motions of E. coli ribonuclease H by Monte Carlo simulations. Proteins. 34:1999;533-539.
-
(1999)
Proteins
, vol.34
, pp. 533-539
-
-
Haliloglu, T.1
-
43
-
-
0029919190
-
Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term for simulation and threading
-
Miyazawa S., Jernigan R.L. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term for simulation and threading. J Mol Biol. 256:1996;623-644.
-
(1996)
J Mol Biol
, vol.256
, pp. 623-644
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
44
-
-
0033566614
-
An empirical energy potential with a reference state for protein folding and sequence recognition
-
Miyazawa S., Jernigan R.L. An empirical energy potential with a reference state for protein folding and sequence recognition. Proteins. 36:1999;357-369.
-
(1999)
Proteins
, vol.36
, pp. 357-369
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
45
-
-
0033120251
-
Protein tertiary structure prediction using a branch and bound algorithm
-
Eyrich V.A., Standley D.M., Felts A.K., Friesner R.A. Protein tertiary structure prediction using a branch and bound algorithm. Proteins. 35:1999;41-57.
-
(1999)
Proteins
, vol.35
, pp. 41-57
-
-
Eyrich, V.A.1
Standley, D.M.2
Felts, A.K.3
Friesner, R.A.4
-
46
-
-
0032929780
-
Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins
-
Simons K.T., Ruczinski I., Kooperberg C., Fox B.A., Bystroff C., Baker D. Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins. 34:1999;82-95.
-
(1999)
Proteins
, vol.34
, pp. 82-95
-
-
Simons, K.T.1
Ruczinski, I.2
Kooperberg, C.3
Fox, B.A.4
Bystroff, C.5
Baker, D.6
-
47
-
-
0032612579
-
Ab initio protein structure prediction of CASP III targets using ROSETTA
-
Simons K.T., Bonneau R., Ruczinski I., Baker D. Ab initio protein structure prediction of CASP III targets using ROSETTA. Proteins. (suppl 3):1999;171-176.
-
(1999)
Proteins
, Issue.SUPPL. 3
, pp. 171-176
-
-
Simons, K.T.1
Bonneau, R.2
Ruczinski, I.3
Baker, D.4
-
48
-
-
0032734515
-
Experiment and theory highlight role of native topology in SH3 folding
-
Riddle D.S., Grantcharova V.P., Santiago J.V., Alm E., Ruczinski I., Baker D. Experiment and theory highlight role of native topology in SH3 folding. Nat Struct Biol. 6:1999;1016-1023.
-
(1999)
Nat Struct Biol
, vol.6
, pp. 1016-1023
-
-
Riddle, D.S.1
Grantcharova, V.P.2
Santiago, J.V.3
Alm, E.4
Ruczinski, I.5
Baker, D.6
-
49
-
-
0033411289
-
Prediction of protein structure using a knowledge-based off-lattice united-residue force field and global optimization methods
-
Liwo A., Pillardy J., Kazmierkiewicz R., Wawak R.J., Groth M., Czaplewski C., Oldziej S., Scheraga H.A. Prediction of protein structure using a knowledge-based off-lattice united-residue force field and global optimization methods. Theor Chem Acc. 101:1999;16-20.
-
(1999)
Theor Chem Acc
, vol.101
, pp. 16-20
-
-
Liwo, A.1
Pillardy, J.2
Kazmierkiewicz, R.3
Wawak, R.J.4
Groth, M.5
Czaplewski, C.6
Oldziej, S.7
Scheraga, H.A.8
-
50
-
-
0032605909
-
Calculation of protein conformation by global optimization of a potential energy function
-
Lee J., Liwo A., Ripoll D.L., Pillardy J., Scheraga H.A. Calculation of protein conformation by global optimization of a potential energy function. Proteins. (suppl 3):1999;204-208.
-
(1999)
Proteins
, Issue.SUPPL. 3
, pp. 204-208
-
-
Lee, J.1
Liwo, A.2
Ripoll, D.L.3
Pillardy, J.4
Scheraga, H.A.5
-
51
-
-
0033514939
-
Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field
-
Lee J., Liwo A., Scheraga H.A. Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field. Proc Natl Acad Sci USA. 96:1999;2025-2030.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 2025-2030
-
-
Lee, J.1
Liwo, A.2
Scheraga, H.A.3
-
52
-
-
0032975718
-
De novo simulation of the folding thermodynamics of the GCN4 leucine zipper
-
Mohanty D., Kolinski A., Skolnick J. De novo simulation of the folding thermodynamics of the GCN4 leucine zipper. Biophys J. 77:1999;54-69.
-
(1999)
Biophys J
, vol.77
, pp. 54-69
-
-
Mohanty, D.1
Kolinski, A.2
Skolnick, J.3
-
53
-
-
0033152803
-
Correlation between knowledge-based and detailed atomic potentials
-
Mohanty D., Dominy B.N., Kolinski A., Brooks C.L. III, Skolnick J. Correlation between knowledge-based and detailed atomic potentials. Proteins. 35:1999;447-452.
-
(1999)
Proteins
, vol.35
, pp. 447-452
-
-
Mohanty, D.1
Dominy, B.N.2
Kolinski, A.3
Brooks C.L. III4
Skolnick, J.5
-
54
-
-
0032620117
-
Improved ab initio predictions with a simplified, flexible geometry model
-
Osguthorpe D.J. Improved ab initio predictions with a simplified, flexible geometry model. Proteins. (suppl 3):1999;186-193.
-
(1999)
Proteins
, Issue.SUPPL. 3
, pp. 186-193
-
-
Osguthorpe, D.J.1
-
55
-
-
0032488962
-
An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction
-
Samudrala R., Moult J. An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. J Mol Biol. 275:1998;895-916.
-
(1998)
J Mol Biol
, vol.275
, pp. 895-916
-
-
Samudrala, R.1
Moult, J.2
-
56
-
-
0032577270
-
A graph-theoretic algorithm for comparative modeling of protein structure
-
Samudrala R., Moult J. A graph-theoretic algorithm for comparative modeling of protein structure. J Mol Biol. 279:1998;287-302.
-
(1998)
J Mol Biol
, vol.279
, pp. 287-302
-
-
Samudrala, R.1
Moult, J.2
-
57
-
-
0031794714
-
Determinants of side chain conformational preferences in protein structures
-
Samudrala R., Moult J. Determinants of side chain conformational preferences in protein structures. Protein Eng. 11:1998;991-997.
-
(1998)
Protein Eng
, vol.11
, pp. 991-997
-
-
Samudrala, R.1
Moult, J.2
-
58
-
-
0032606133
-
Ab initio protein structure prediction using a combined hierarchical approach
-
Samudrala R., Xia Y., Huang E., Levitt M. Ab initio protein structure prediction using a combined hierarchical approach. Proteins. (suppl 3):1999;194-198.
-
(1999)
Proteins
, Issue.SUPPL. 3
, pp. 194-198
-
-
Samudrala, R.1
Xia, Y.2
Huang, E.3
Levitt, M.4
-
59
-
-
0032540222
-
Assessing proteins structures with a nonlocal atomic interaction energy
-
Melo F., Feytmans E. Assessing proteins structures with a nonlocal atomic interaction energy. J Mol Biol. 277:1998;1141-1152.
-
(1998)
J Mol Biol
, vol.277
, pp. 1141-1152
-
-
Melo, F.1
Feytmans, E.2
-
60
-
-
0033168866
-
Knowledge-based interaction potentials for proteins
-
Rojnuckarin A., Subramaniam S. Knowledge-based interaction potentials for proteins. Proteins. 36:1999;54-67.
-
(1999)
Proteins
, vol.36
, pp. 54-67
-
-
Rojnuckarin, A.1
Subramaniam, S.2
-
61
-
-
0032790342
-
Protein fold recognition score functions. Unusual construction strategies
-
Ayers D.J., Huber T., Torda A.E. Protein fold recognition score functions. Unusual construction strategies. Proteins. 36:1999;454-461.
-
(1999)
Proteins
, vol.36
, pp. 454-461
-
-
Ayers, D.J.1
Huber, T.2
Torda, A.E.3
-
62
-
-
0000817556
-
Protein sequence threading, the alignment problem and a two step strategy
-
Huber A., Torda A.E. Protein sequence threading, the alignment problem and a two step strategy. J Comput Chem. 20:1999;1455-1467.
-
(1999)
J Comput Chem
, vol.20
, pp. 1455-1467
-
-
Huber, A.1
Torda, A.E.2
-
64
-
-
0000779818
-
Poisson-Boltzmann analytical gradients for molecular modeling calculations
-
Friedrichs M., Zhou R., Edinger R., Friesner R.A. Poisson-Boltzmann analytical gradients for molecular modeling calculations. J Phys Chem B. 103:1999;3057-3061.
-
(1999)
J Phys Chem B
, vol.103
, pp. 3057-3061
-
-
Friedrichs, M.1
Zhou, R.2
Edinger, R.3
Friesner, R.A.4
-
65
-
-
0032968133
-
Implicit solvent models
-
Roux R., Simonson T. Implicit solvent models. Biophys Chem. 78:1999;1-20.
-
(1999)
Biophys Chem
, vol.78
, pp. 1-20
-
-
Roux, R.1
Simonson, T.2
-
66
-
-
0033003955
-
ES/IS: Estimation of conformational free energy by combining dynamics simulations with explicit solvent with an implicit solvent continuum model
-
Vorobjev Y.N., Hermans J. ES/IS: estimation of conformational free energy by combining dynamics simulations with explicit solvent with an implicit solvent continuum model. Biophys Chem. 78:1999;195-205.
-
(1999)
Biophys Chem
, vol.78
, pp. 195-205
-
-
Vorobjev, Y.N.1
Hermans, J.2
-
67
-
-
0001546192
-
Solvations: A semi-empirical procedure for including solvation in quantum mechanical calculations of large molecules
-
Klopman G. Solvations: a semi-empirical procedure for including solvation in quantum mechanical calculations of large molecules. Chem Phys Lett. 1:1967;200-202.
-
(1967)
Chem Phys Lett
, vol.1
, pp. 200-202
-
-
Klopman, G.1
-
68
-
-
85047691965
-
Self consistent field theory of solvent effects representation by continuum models: Introduction of desolvation contribution
-
Constanciel R., Contreras R. Self consistent field theory of solvent effects representation by continuum models: introduction of desolvation contribution. Theor Chim Acta. 65:1984;1-11.
-
(1984)
Theor Chim Acta
, vol.65
, pp. 1-11
-
-
Constanciel, R.1
Contreras, R.2
-
69
-
-
0000536249
-
Generalized Born fragment charge model for solvation effects as a function of reaction coordinate
-
Tucker S.C., Truhlar D.G. Generalized Born fragment charge model for solvation effects as a function of reaction coordinate. Chem Phys Lett. 157:1989;164-170.
-
(1989)
Chem Phys Lett
, vol.157
, pp. 164-170
-
-
Tucker, S.C.1
Truhlar, D.G.2
-
70
-
-
0344778061
-
Semianalytical treatment of solvation for molecular mechanics and dynamics
-
Still W.C., Tempczyk A., Hawley R.C., Hendrickson T. Semianalytical treatment of solvation for molecular mechanics and dynamics. J Am Chem Soc. 112:1990;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
-
71
-
-
0012227656
-
A comprehensive analytical treatment of continuum electrostatics
-
Schaefer M., Karplus M. A comprehensive analytical treatment of continuum electrostatics. J Phys Chem. 100:1996;1578-1599.
-
(1996)
J Phys Chem
, vol.100
, pp. 1578-1599
-
-
Schaefer, M.1
Karplus, M.2
-
72
-
-
0032484151
-
Solution conformations and thermodynamics of structured peptides: Molecular dynamics simulation with an implicit solvation model
-
Schaefer M., Bartels C., Karplus M. Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model. J Mol Biol. 284:1998;835-847.
-
(1998)
J Mol Biol
, vol.284
, pp. 835-847
-
-
Schaefer, M.1
Bartels, C.2
Karplus, M.3
-
73
-
-
4043171970
-
The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii
-
Qiu D., Shenkin P.S., Hollinger F.P., Still W.C. The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii. J Phys Chem A. 101:1997;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
-
74
-
-
84961985307
-
Development of a generalized Born model parameterization for proteins and nucleic acids
-
Dominy B.N., Brooks C.L. III Development of a generalized Born model parameterization for proteins and nucleic acids. J Phys Chem B. 103:1999;3765-3773.
-
(1999)
J Phys Chem B
, vol.103
, pp. 3765-3773
-
-
Dominy, B.N.1
Brooks C.L. III2
-
75
-
-
0022596727
-
Solvation energy in protein folding and binding
-
Eisenberg D., McLachlan A.D. Solvation energy in protein folding and binding. Nature. 319:1986;199-203.
-
(1986)
Nature
, vol.319
, pp. 199-203
-
-
Eisenberg, D.1
McLachlan, A.D.2
-
76
-
-
0033042625
-
Heat capacity and compactness of denatured proteins
-
Lazaridis T., Karplus M. Heat capacity and compactness of denatured proteins. Biophys Chem. 78:1999;207-217.
-
(1999)
Biophys Chem
, vol.78
, pp. 207-217
-
-
Lazaridis, T.1
Karplus, M.2
-
77
-
-
0027299504
-
Towards protein folding by global energy optimization
-
Abagyan R. Towards protein folding by global energy optimization. FEBS Lett. 325:1993;17-22.
-
(1993)
FEBS Lett
, vol.325
, pp. 17-22
-
-
Abagyan, R.1
-
78
-
-
0032828469
-
Analysis and assessment of ab initio three-dimensional prediction, secondary structure and contacts prediction
-
Orengo C.A., Bray J.E., Hubbard T., LoConte L., Sillitoe I. Analysis and assessment of ab initio three-dimensional prediction, secondary structure and contacts prediction. Protein. (suppl 3):1999;149-170.
-
(1999)
Protein
, Issue.SUPPL. 3
, pp. 149-170
-
-
Orengo, C.A.1
Bray, J.E.2
Hubbard, T.3
Loconte, L.4
Sillitoe, I.5
|