-
2
-
-
3042693653
-
Cluster distance geometry of polypeptide chains
-
Grippen GM. Cluster distance geometry of polypeptide chains. J Comput Chem 2004;25:1305-1312.
-
(2004)
J Comput Chem
, vol.25
, pp. 1305-1312
-
-
Grippen, G.M.1
-
3
-
-
7044240651
-
Statistical mechanics of protein folding by cluster distance geometry
-
Grippen GM. Statistical mechanics of protein folding by cluster distance geometry. Biopolymers 2004;75:278-289.
-
(2004)
Biopolymers
, vol.75
, pp. 278-289
-
-
Grippen, G.M.1
-
4
-
-
33845377127
-
Estimation of effective contact energies from protein crystal structures: Quasi-chemical approximation
-
Miyazawa S, Jernigan RL. Estimation of effective contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules 1985;18:534-552.
-
(1985)
Macromolecules
, vol.18
, pp. 534-552
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
5
-
-
0026655922
-
Protein tertiary structure recognition using optimized hamiltonians with local interactions
-
Goldstein RA, Luthey-Schulten Z, Wolynes PG. Protein tertiary structure recognition using optimized hamiltonians with local interactions. Proc Natl Acad Sci USA 1992;89:9029-9033.
-
(1992)
Proc Natl Acad Sci USA
, vol.89
, pp. 9029-9033
-
-
Goldstein, R.A.1
Luthey-Schulten, Z.2
Wolynes, P.G.3
-
6
-
-
0026785519
-
Contact potential that recognizes the correct folding of globular proteins
-
Maiorov VN, Crippen GM. Contact potential that recognizes the correct folding of globular proteins. J Mol Biol 1992;227:876-888.
-
(1992)
J Mol Biol
, vol.227
, pp. 876-888
-
-
Maiorov, V.N.1
Crippen, G.M.2
-
7
-
-
0027650879
-
Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination f protein structures
-
Sippl MJ. Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination f protein structures. J Comput-Aided Mol Design 1993;7:473-501.
-
(1993)
J Comput-Aided Mol Design
, vol.7
, pp. 473-501
-
-
Sippl, M.J.1
-
8
-
-
0028149160
-
Exploring conformational space with a simple lattice model for protein structure
-
Hinds DA, Levitt M. Exploring conformational space with a simple lattice model for protein structure. J Mol Biol 1994;243:668-682.
-
(1994)
J Mol Biol
, vol.243
, pp. 668-682
-
-
Hinds, D.A.1
Levitt, M.2
-
9
-
-
0028318094
-
Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches
-
Kocher J-PA, Rooman MJ, Wodak SJ. Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches. J Mol Biol 1994;235:1598-1613.
-
(1994)
J Mol Biol
, vol.235
, pp. 1598-1613
-
-
Kocher, J.-P.A.1
Rooman, M.J.2
Wodak, S.J.3
-
10
-
-
0028892389
-
Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets
-
Godzik A, Kolinski A, Skolnick J. Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets. Protein Sci 1995;4:2107-2117.
-
(1995)
Protein Sci
, vol.4
, pp. 2107-2117
-
-
Godzik, A.1
Kolinski, A.2
Skolnick, J.3
-
11
-
-
0030596063
-
How to derive a protein folding potential? A new approach to an old problem
-
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.
-
(1996)
J Mol Biol
, vol.264
, pp. 1164-1179
-
-
Mirny, L.A.1
Shakhnovich, E.I.2
-
12
-
-
0029919190
-
Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term for simulation and threading
-
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.
-
(1996)
J Mol Biol
, vol.256
, pp. 623-644
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
13
-
-
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;258: 367-392.
-
(1996)
J Mol Biol
, vol.258
, pp. 367-392
-
-
Park, B.1
Levitt, M.2
-
14
-
-
0031557390
-
Factors affecting the ability of energy functions to discriminate correct from incorrect folds
-
Park BH, Huang ES, Levitt M. Factors affecting the ability of energy functions to discriminate correct from incorrect folds. J Mol Biol 1997;266:831-846.
-
(1997)
J Mol Biol
, vol.266
, pp. 831-846
-
-
Park, B.H.1
Huang, E.S.2
Levitt, M.3
-
15
-
-
0030983768
-
Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct?
-
Skolnick J, Jaroszewski L, Kolinski A, Godzik A. Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct? Protein Sci 1997;6:676-688.
-
(1997)
Protein Sci
, vol.6
, pp. 676-688
-
-
Skolnick, J.1
Jaroszewski, L.2
Kolinski, A.3
Godzik, A.4
-
16
-
-
0000171351
-
Pairwise contact potentials are unsuitable for protein folding
-
Vendruscolo M, Domany E. Pairwise contact potentials are unsuitable for protein folding. J Chem Phys 1998;109:1101-1108.
-
(1998)
J Chem Phys
, vol.109
, pp. 1101-1108
-
-
Vendruscolo, M.1
Domany, E.2
-
17
-
-
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 1998;275:895-916.
-
(1998)
J Mol Biol
, vol.275
, pp. 895-916
-
-
Samudrala, R.1
Moult, J.2
-
19
-
-
0034308163
-
Distance-dependent pair potential for protein folding: Results from linear optimization
-
Tobi D, Elber R. Distance-dependent pair potential for protein folding: results from linear optimization. Proteins 2000;41:40-46.
-
(2000)
Proteins
, vol.41
, pp. 40-46
-
-
Tobi, D.1
Elber, R.2
-
20
-
-
0034237798
-
On the design and analysis of protein folding potentials
-
Tobi D, Shafran G, Linial N, Elber R. On the design and analysis of protein folding potentials. Proteins 2000;40:71-85.
-
(2000)
Proteins
, vol.40
, pp. 71-85
-
-
Tobi, D.1
Shafran, G.2
Linial, N.3
Elber, R.4
-
21
-
-
0034141931
-
Can a pairwise contact potential stabilize native protein folds against decoys obtained by threading?
-
Vendruscolo M, Najmanovich R, Domany E. Can a pairwise contact potential stabilize native protein folds against decoys obtained by threading? Proteins 2000;38:134-148.
-
(2000)
Proteins
, vol.38
, pp. 134-148
-
-
Vendruscolo, M.1
Najmanovich, R.2
Domany, E.3
-
22
-
-
0034529140
-
Disulfide recognition in an optimized threading potential
-
Dombkowski AA, Crippen GM. Disulfide recognition in an optimized threading potential. Protein Eng 2000;13:679-689.
-
(2000)
Protein Eng
, vol.13
, pp. 679-689
-
-
Dombkowski, A.A.1
Crippen, G.M.2
-
23
-
-
0033693249
-
Potential energy function for continuous state model of globular proteins
-
Ohkubo YZ, Crippen GM. Potential energy function for continuous state model of globular proteins. J Comput Biol 2000;7:363-379.
-
(2000)
J Comput Biol
, vol.7
, pp. 363-379
-
-
Ohkubo, Y.Z.1
Crippen, G.M.2
-
24
-
-
0035002440
-
Constructing smooth potential functions for protein folding
-
Crippen GM. Constructing smooth potential functions for protein folding. J Mol Graph Mod 2001;19:87-93.
-
(2001)
J Mol Graph Mod
, vol.19
, pp. 87-93
-
-
Crippen, G.M.1
-
25
-
-
0028895567
-
Discriminating compact nonnative structures from the native structure of globular proteins
-
Wang Y, Zhang H, Li W, Scott RA. Discriminating compact nonnative structures from the native structure of globular proteins. Proc Natl Acad Sci USA 1995;92:709-713.
-
(1995)
Proc Natl Acad Sci USA
, vol.92
, pp. 709-713
-
-
Wang, Y.1
Zhang, H.2
Li, W.3
Scott, R.A.4
-
26
-
-
0029871791
-
Using a hydrophobic contact potential to evaluate native and near-native folds generated by molecular dynamics simulations
-
Huang ES, Subbiah S, Tsai J, Levitt M. Using a hydrophobic contact potential to evaluate native and near-native folds generated by molecular dynamics simulations. J Mol Biol 1996;257:716-725.
-
(1996)
J Mol Biol
, vol.257
, pp. 716-725
-
-
Huang, E.S.1
Subbiah, S.2
Tsai, J.3
Levitt, M.4
-
27
-
-
0031821113
-
Statistical mechanics of protein folding by exhaustive enumeration
-
Crippen GM, Ohkubo YZ. Statistical mechanics of protein folding by exhaustive enumeration. Proteins 1998;32:425-437.
-
(1998)
Proteins
, vol.32
, pp. 425-437
-
-
Crippen, G.M.1
Ohkubo, Y.Z.2
-
28
-
-
0035865950
-
Learning effective amino acid interactions through interactive stochastic techniques
-
Micheletti C, Seno F, Banavar JR, Maritan A. Learning effective amino acid interactions through interactive stochastic techniques. Proteins 2001;42:422-431.
-
(2001)
Proteins
, vol.42
, pp. 422-431
-
-
Micheletti, C.1
Seno, F.2
Banavar, J.R.3
Maritan, A.4
-
29
-
-
4043173536
-
Toward correct protein folding potentials
-
Chhajer M, Crippen GM. Toward correct protein folding potentials. J Biol Phys 2004;30:171-185.
-
(2004)
J Biol Phys
, vol.30
, pp. 171-185
-
-
Chhajer, M.1
Crippen, G.M.2
-
30
-
-
0033954256
-
The Protein Data Bank
-
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.
-
(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
-
33
-
-
0036084625
-
SCOP database in 2002: Refinements accommodate structural genomics
-
Lo Conte L, Brenner SE, Hubbard TJP, Chothia C, Murzin A. SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acid Res 2002;30:264-267.
-
(2002)
Nucleic Acid Res
, vol.30
, pp. 264-267
-
-
Lo Conte, L.1
Brenner, S.E.2
Hubbard, T.J.P.3
Chothia, C.4
Murzin, A.5
-
34
-
-
0029057126
-
Size-independent comparison of protein three-dimensional structures
-
Maiorov VN, Crippen GM. Size-independent comparison of protein three-dimensional structures. Proteins 1995;22:273-283.
-
(1995)
Proteins
, vol.22
, pp. 273-283
-
-
Maiorov, V.N.1
Crippen, G.M.2
|