-
1
-
-
0030914617
-
Comparison of database potentials and molecular mechanics force fields
-
10.1016/S0959-440X(97)80025-5, 9094335
-
Moult J. Comparison of database potentials and molecular mechanics force fields. Curr Opin Struct Biol 1997, 7:194-199. 10.1016/S0959-440X(97)80025-5, 9094335.
-
(1997)
Curr Opin Struct Biol
, vol.7
, pp. 194-199
-
-
Moult, J.1
-
2
-
-
0030968991
-
Empirical potentials and functions for protein folding and binding
-
10.1016/S0959-440X(97)80029-2, 9094333
-
Vajda S, Sippl M, Novotny J. Empirical potentials and functions for protein folding and binding. Curr Opin Struct Biol 1997, 7:222-228. 10.1016/S0959-440X(97)80029-2, 9094333.
-
(1997)
Curr Opin Struct Biol
, vol.7
, pp. 222-228
-
-
Vajda, S.1
Sippl, M.2
Novotny, J.3
-
3
-
-
0030596063
-
How to derive a protein folding potential? A new approach to an old problem
-
10.1006/jmbi.1996.0704, 9000638
-
Mirny LA, Shakhnovich EI. How to derive a protein folding potential? A new approach to an old problem. J Mol Biol 1996, 264:1164-1179. 10.1006/jmbi.1996.0704, 9000638.
-
(1996)
J Mol Biol
, vol.264
, pp. 1164-1179
-
-
Mirny, L.A.1
Shakhnovich, E.I.2
-
4
-
-
0033117762
-
Designing potential energy functions for protein folding
-
10.1016/S0959-440X(99)80026-8, 10322206
-
Hao MH, Scheraga HA. Designing potential energy functions for protein folding. Curr Opin Struct Biol 1999, 9:184-188. 10.1016/S0959-440X(99)80026-8, 10322206.
-
(1999)
Curr Opin Struct Biol
, vol.9
, pp. 184-188
-
-
Hao, M.H.1
Scheraga, H.A.2
-
5
-
-
0033566614
-
An empirical energy potential with a reference state for protein fold and sequence recognition
-
10.1002/(SICI)1097-0134(19990815)36:3<357::AID-PROT10>3.0.CO;2-U, 10409829
-
Miyazawa S, Jernigan RL. An empirical energy potential with a reference state for protein fold and sequence recognition. Proteins 1999, 36:357-369. 10.1002/(SICI)1097-0134(19990815)36:3<357::AID-PROT10>3.0.CO;2-U, 10409829.
-
(1999)
Proteins
, vol.36
, pp. 357-369
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
6
-
-
0034031680
-
Effective energy functions for protein structure prediction
-
Lazaridis T, Karplus M. Effective energy functions for protein structure prediction. Curr Opin Struct Biol 2000, 10:145.
-
(2000)
Curr Opin Struct Biol
, vol.10
, pp. 145
-
-
Lazaridis, T.1
Karplus, M.2
-
7
-
-
0036681394
-
Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all-atom force field and the Surface Generalized Born solvent model
-
10.1002/prot.10171, 12112706
-
Felts AK, Gallicchio E, Wallqvist A, Levy RM. Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all-atom force field and the Surface Generalized Born solvent model. Proteins 2002, 48:404-422. 10.1002/prot.10171, 12112706.
-
(2002)
Proteins
, vol.48
, pp. 404-422
-
-
Felts, A.K.1
Gallicchio, E.2
Wallqvist, A.3
Levy, R.M.4
-
8
-
-
0037079585
-
Identifying native-like protein structures using physics-based potentials
-
10.1002/jcc.10018, 11913380
-
Dominy BN, Brooks CL. Identifying native-like protein structures using physics-based potentials. J Comput Chem 2002, 23:147-160. 10.1002/jcc.10018, 11913380.
-
(2002)
J Comput Chem
, vol.23
, pp. 147-160
-
-
Dominy, B.N.1
Brooks, C.L.2
-
9
-
-
0033531959
-
Discrimination of the native from misfolded protein models with an energy function including implicit solvation
-
10.1006/jmbi.1999.2685, 10329155
-
Lazaridis T, Karplus M. Discrimination of the native from misfolded protein models with an energy function including implicit solvation. J Mol Biol 1999, 288:477-487. 10.1006/jmbi.1999.2685, 10329155.
-
(1999)
J Mol Biol
, vol.288
, pp. 477-487
-
-
Lazaridis, T.1
Karplus, M.2
-
10
-
-
0033537993
-
GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences
-
10.1006/jmbi.1999.2583, 10191147
-
Jones DT. GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J Mol Biol 1999, 287:797-815. 10.1006/jmbi.1999.2583, 10191147.
-
(1999)
J Mol Biol
, vol.287
, pp. 797-815
-
-
Jones, D.T.1
-
11
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
-
Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 1983, 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.6
-
12
-
-
0033135638
-
Effective energy function for proteins in solution. Proteins
-
10.1002/(SICI)1097-0134(19990501)35:2<133::AID-PROT1>3.0.CO;2-N, 10223287
-
Lazaridis T, Karplus M. Effective energy function for proteins in solution. Proteins. Proteins 1999, 35:133-152. 10.1002/(SICI)1097-0134(19990501)35:2<133::AID-PROT1>3.0.CO;2-N, 10223287.
-
(1999)
Proteins
, vol.35
, pp. 133-152
-
-
Lazaridis, T.1
Karplus, M.2
-
13
-
-
0021757436
-
A new force field for molecular mechanical simulation of nucleic acids and proteins
-
Weiner SJ, Kollman PA, Case DA, Singh UC, Ghio C, Alagona G. A new force field for molecular mechanical simulation of nucleic acids and proteins. J Am Chem Soc 1984, 106:765-787.
-
(1984)
J Am Chem Soc
, vol.106
, pp. 765-787
-
-
Weiner, S.J.1
Kollman, P.A.2
Case, D.A.3
Singh, U.C.4
Ghio, C.5
Alagona, G.6
-
14
-
-
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, 118:11225-111236.
-
(1996)
J Am Chem Soc
, vol.118
, pp. 11225-111236
-
-
Jorgensen, W.L.1
Maxwell, D.S.2
Tirado-Rives, J.3
-
15
-
-
0025341310
-
Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins
-
10.1016/S0022-2836(05)80269-4, 2359125
-
Sippl MJ. Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. J Mol Biol 1990, 213:859-883. 10.1016/S0022-2836(05)80269-4, 2359125.
-
(1990)
J Mol Biol
, vol.213
, pp. 859-883
-
-
Sippl, M.J.1
-
16
-
-
0029000696
-
Knowledge-based potentials for proteins
-
10.1016/0959-440X(95)80081-6, 7648326
-
Sippl MJ. Knowledge-based potentials for proteins. Curr Opin Struct Biol 1995, 5:229-235. 10.1016/0959-440X(95)80081-6, 7648326.
-
(1995)
Curr Opin Struct Biol
, vol.5
, pp. 229-235
-
-
Sippl, M.J.1
-
17
-
-
0026761547
-
Folding protein alpha-carbon chains into compact forms by Monte Carlo methods
-
10.1002/prot.340140310, 1438179
-
Covell DG. Folding protein alpha-carbon chains into compact forms by Monte Carlo methods. Proteins 1992, 14:409-420. 10.1002/prot.340140310, 1438179.
-
(1992)
Proteins
, vol.14
, pp. 409-420
-
-
Covell, D.G.1
-
18
-
-
0027503403
-
Reduced representation model of protein structure prediction: statistical potential and genetic algorithms
-
10.1002/pro.5560020508, 2142494, 8495198
-
Sun S. Reduced representation model of protein structure prediction: statistical potential and genetic algorithms. Protein Sci 1993, 2:762-785. 10.1002/pro.5560020508, 2142494, 8495198.
-
(1993)
Protein Sci
, vol.2
, pp. 762-785
-
-
Sun, S.1
-
19
-
-
0028351287
-
An improved pair potential to recognize native protein folds
-
10.1002/prot.340180306, 8202466
-
Bauer A, Beyer A. An improved pair potential to recognize native protein folds. Proteins 1994, 18:254-261. 10.1002/prot.340180306, 8202466.
-
(1994)
Proteins
, vol.18
, pp. 254-261
-
-
Bauer, A.1
Beyer, A.2
-
20
-
-
0029942661
-
Structure-derived potentials and protein simulations
-
10.1016/S0959-440X(96)80075-3, 8728652
-
Jernigan RL, Bahar I. Structure-derived potentials and protein simulations. Curr Opin Struct Biol 1996, 6:195-209. 10.1016/S0959-440X(96)80075-3, 8728652.
-
(1996)
Curr Opin Struct Biol
, vol.6
, pp. 195-209
-
-
Jernigan, R.L.1
Bahar, I.2
-
21
-
-
0032540222
-
Assessing protein structures with a non-local atomic interaction energy
-
10.1006/jmbi.1998.1665, 9571028
-
Melo F, Feytmans E. Assessing protein structures with a non-local atomic interaction energy. J Mol Biol 1998, 277:1141-1152. 10.1006/jmbi.1998.1665, 9571028.
-
(1998)
J Mol Biol
, vol.277
, pp. 1141-1152
-
-
Melo, F.1
Feytmans, E.2
-
22
-
-
0034308163
-
Distance-dependent, pair potential for protein folding: Results from linear optimization
-
10.1002/1097-0134(20001001)41:1<40::AID-PROT70>3.0.CO;2-U, 10944392
-
Tobi D, Elber R. Distance-dependent, pair potential for protein folding: Results from linear optimization. Proteins 2000, 41:40-46. 10.1002/1097-0134(20001001)41:1<40::AID-PROT70>3.0.CO;2-U, 10944392.
-
(2000)
Proteins
, vol.41
, pp. 40-46
-
-
Tobi, D.1
Elber, R.2
-
23
-
-
0036145846
-
Statistical potentials for fold assessment
-
10.1110/ps.25502, 2373452, 11790853
-
Melo F, Sanchez R, Sali A. Statistical potentials for fold assessment. Protein Sci 2002, 11:430-448. 10.1110/ps.25502, 2373452, 11790853.
-
(2002)
Protein Sci
, vol.11
, pp. 430-448
-
-
Melo, F.1
Sanchez, R.2
Sali, A.3
-
24
-
-
33747135021
-
Novel knowledge-based mean force potential at the profile level
-
10.1186/1471-2105-7-324, 1534065, 16803615
-
Dong Q, Wang X, Lin L. Novel knowledge-based mean force potential at the profile level. BMC Bioinformatics 2006, 7:324. 10.1186/1471-2105-7-324, 1534065, 16803615.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 324
-
-
Dong, Q.1
Wang, X.2
Lin, L.3
-
25
-
-
0042921442
-
How well can we predict native contacts in proteins based on decoy structures and their energies?
-
10.1002/prot.10444, 12910459
-
Zhu J, Zhu Q, Shi Y, Liu H. How well can we predict native contacts in proteins based on decoy structures and their energies?. Proteins 2003, 52:598-608. 10.1002/prot.10444, 12910459.
-
(2003)
Proteins
, vol.52
, pp. 598-608
-
-
Zhu, J.1
Zhu, Q.2
Shi, Y.3
Liu, H.4
-
26
-
-
0037452894
-
Discrimination of native protein structures using atom-atom contact scoring
-
McConkey BJ, Sobolev V, Edelman M. Discrimination of native protein structures using atom-atom contact scoring. Proc Natl Acad Sci U S A 2003, 100:3215-3220.
-
(2003)
Proc Natl Acad Sci U S A
, vol.100
, pp. 3215-3220
-
-
McConkey, B.J.1
Sobolev, V.2
Edelman, M.3
-
27
-
-
1642534609
-
An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state
-
10.1110/ps.03348304, 2286718, 14739325
-
Zhang C, Liu S, Zhou H, Zhou Y. An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state. Protein Sci 2004, 13:400-411. 10.1110/ps.03348304, 2286718, 14739325.
-
(2004)
Protein Sci
, vol.13
, pp. 400-411
-
-
Zhang, C.1
Liu, S.2
Zhou, H.3
Zhou, Y.4
-
28
-
-
33645792604
-
Physically realistic homology models built with ROSETTA can be more accurate than their templates
-
10.1073/pnas.0509355103, 1459360, 16567638
-
Misura KM, Chivian D, Rohl CA, Kim DE, Baker D. Physically realistic homology models built with ROSETTA can be more accurate than their templates. Proc Natl Acad Sci 2006, 103:5361-5366. 10.1073/pnas.0509355103, 1459360, 16567638.
-
(2006)
Proc Natl Acad Sci
, vol.103
, pp. 5361-5366
-
-
Misura, K.M.1
Chivian, D.2
Rohl, C.A.3
Kim, D.E.4
Baker, D.5
-
29
-
-
0031585984
-
Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
-
10.1006/jmbi.1997.0959, 9149153
-
Simons KT, 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 1997, 268:209-225. 10.1006/jmbi.1997.0959, 9149153.
-
(1997)
J Mol Biol
, vol.268
, pp. 209-225
-
-
Simons, K.T.1
Kooperberg, C.2
Huang, E.3
Baker, D.4
-
30
-
-
33749578940
-
Statistical potential for assessment and prediction of protein structures
-
10.1110/ps.062416606, 2242414, 17075131
-
Shen MY, Sali A. Statistical potential for assessment and prediction of protein structures. Protein Sci 2006, 15:2507-2524. 10.1110/ps.062416606, 2242414, 17075131.
-
(2006)
Protein Sci
, vol.15
, pp. 2507-2524
-
-
Shen, M.Y.1
Sali, A.2
-
31
-
-
34247356171
-
Scoring predictive models using a reduced representation of proteins: model and energy definition
-
10.1186/1472-6807-7-15, 1854906, 17378941
-
Fogolari F, Pieri L, Dovier A, Bortolussi L, Giugliarelli G, Corazza A, Esposito G, Viglino P. Scoring predictive models using a reduced representation of proteins: model and energy definition. BMC Struct Biol 2007, 7:15. 10.1186/1472-6807-7-15, 1854906, 17378941.
-
(2007)
BMC Struct Biol
, vol.7
, pp. 15
-
-
Fogolari, F.1
Pieri, L.2
Dovier, A.3
Bortolussi, L.4
Giugliarelli, G.5
Corazza, A.6
Esposito, G.7
Viglino, P.8
-
32
-
-
70349448457
-
A distance-dependent atomic knowledge-based potential and force for discrimination of native structures from decoys
-
10.1002/prot.22457, 19452553
-
Mirzaie M, Eslahchi C, Pezeshk H, Sadeghi M. A distance-dependent atomic knowledge-based potential and force for discrimination of native structures from decoys. Proteins 2009, 77:454-463. 10.1002/prot.22457, 19452553.
-
(2009)
Proteins
, vol.77
, pp. 454-463
-
-
Mirzaie, M.1
Eslahchi, C.2
Pezeshk, H.3
Sadeghi, M.4
-
33
-
-
0344980731
-
Simplicial edge representation of protein structures and alpha contact potential with confidence measure
-
10.1002/prot.10442, 14635122
-
Li X, Hu C, Liang J. Simplicial edge representation of protein structures and alpha contact potential with confidence measure. Proteins 2003, 53:792-805. 10.1002/prot.10442, 14635122.
-
(2003)
Proteins
, vol.53
, pp. 792-805
-
-
Li, X.1
Hu, C.2
Liang, J.3
-
34
-
-
0029919190
-
Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading
-
10.1006/jmbi.1996.0114, 8604144
-
Miyazawa S, Jernigan RL. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J Mol Biol 1996, 256:623-644. 10.1006/jmbi.1996.0114, 8604144.
-
(1996)
J Mol Biol
, vol.256
, pp. 623-644
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
36
-
-
0028205447
-
Enlarged representative set of protein structures
-
2142698, 8019422
-
Hobohm U, Sander C. Enlarged representative set of protein structures. Protein Sci 1994, 3:522-524. 2142698, 8019422.
-
(1994)
Protein Sci
, vol.3
, pp. 522-524
-
-
Hobohm, U.1
Sander, C.2
-
37
-
-
0033954256
-
The Protein Data Bank
-
10.1093/nar/28.1.235, 102472, 10592235
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000, 28:235-242. 10.1093/nar/28.1.235, 102472, 10592235.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
38
-
-
29244479220
-
A decoy set for the thermostable subdomain from chicken villin headpiece, comparison of different free energy estimators
-
10.1186/1471-2105-6-301, 1351271, 16354298
-
Fogolari F, Tosatto SC, Colombo G. A decoy set for the thermostable subdomain from chicken villin headpiece, comparison of different free energy estimators. BMC Bioinformatics 2005, 6:301. 10.1186/1471-2105-6-301, 1351271, 16354298.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 301
-
-
Fogolari, F.1
Tosatto, S.C.2
Colombo, G.3
-
39
-
-
0026505184
-
Evaluation of protein models by atomic solvation preference
-
10.1016/0022-2836(92)91028-N, 1583696
-
Holm L, Sander C. Evaluation of protein models by atomic solvation preference. J Mol Biol 1992, 225:93-105. 10.1016/0022-2836(92)91028-N, 1583696.
-
(1992)
J Mol Biol
, vol.225
, pp. 93-105
-
-
Holm, L.1
Sander, C.2
-
40
-
-
3342936478
-
A comprehensive analysis of 40 blind protein structure predictions
-
10.1186/1472-6807-2-3, 122083, 12150712
-
Samudrala R, Levitt M. A comprehensive analysis of 40 blind protein structure predictions. BMC Struct Biol 2002, 2:3-18. 10.1186/1472-6807-2-3, 122083, 12150712.
-
(2002)
BMC Struct Biol
, vol.2
, pp. 3-18
-
-
Samudrala, R.1
Levitt, M.2
-
41
-
-
0033853177
-
Decoys'R' Us:a database of incorrect conformation to improve protein structure prediction
-
10.1110/ps.9.7.1399, 2144680, 10933507
-
Samudrala R, Levitt M. Decoys'R' Us:a database of incorrect conformation to improve protein structure prediction. Protein Sci 2000, 9:1399-1401. 10.1110/ps.9.7.1399, 2144680, 10933507.
-
(2000)
Protein Sci
, vol.9
, pp. 1399-1401
-
-
Samudrala, R.1
Levitt, M.2
-
42
-
-
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 1996, 285:367-392.
-
(1996)
J Mol Biol
, vol.285
, pp. 367-392
-
-
Park, B.1
Levitt, M.2
-
43
-
-
33750050261
-
A novel high resolution Calpha--Calpha distance dependent force field based on a high quality decoy set
-
10.1002/prot.21149, 16981202
-
Rajgaria R, McAllister SR, Floudas CA. A novel high resolution Calpha--Calpha distance dependent force field based on a high quality decoy set. Proteins 2006, 65:726-741. 10.1002/prot.21149, 16981202.
-
(2006)
Proteins
, vol.65
, pp. 726-741
-
-
Rajgaria, R.1
McAllister, S.R.2
Floudas, C.A.3
-
44
-
-
0038008976
-
An improved protein decoy set for testing energy functions for protein structure prediction
-
10.1002/prot.10454, 12945051
-
Tsai J, Bonneau R, Morozov AV, Kuhlman B, Rohl CA, Baker D. An improved protein decoy set for testing energy functions for protein structure prediction. Proteins 2003, 53:76-87. 10.1002/prot.10454, 12945051.
-
(2003)
Proteins
, vol.53
, pp. 76-87
-
-
Tsai, J.1
Bonneau, R.2
Morozov, A.V.3
Kuhlman, B.4
Rohl, C.A.5
Baker, D.6
-
46
-
-
47849103560
-
Decoy Discrimination Using Contact Potentials Based on Delaunay Tessellation of Hydrated Proteins
-
Reck GM, Vaisman II. Decoy Discrimination Using Contact Potentials Based on Delaunay Tessellation of Hydrated Proteins. IEEE Computer Society 2007, 159-167.
-
(2007)
IEEE Computer Society
, pp. 159-167
-
-
Reck, G.M.1
Vaisman, I.I.2
|