-
1
-
-
0017021957
-
Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins
-
Tanaka S, Scheraga HA. Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins. Macromolecules 1976;9:945-50.
-
(1976)
Macromolecules
, vol.9
, pp. 945-950
-
-
Tanaka, S.1
Scheraga, H.A.2
-
2
-
-
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. Nucl Acids Res 2000;28:235-42.
-
(2000)
Nucl 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
-
3
-
-
0033514939
-
Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: Application to the 10-55 fragment of staphylococcal protein A and to Apo Calbindin D9K
-
Lee J, Liwo A, Scheraga HA. Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: application to the 10-55 fragment of staphylococcal protein A and to Apo Calbindin D9K. Proc Natl Acad Sci USA 1999; 96:2025-30.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 2025-2030
-
-
Lee, J.1
Liwo, A.2
Scheraga, H.A.3
-
4
-
-
0032960853
-
Self-consistent estimation of inter-residue protein contact energies based on an equilibrium mixture approximation of residues
-
Miyazawa S, Jernigan RL. Self-consistent estimation of inter-residue protein contact energies based on an equilibrium mixture approximation of residues. Proteins 1999;34:49-68.
-
(1999)
Proteins
, vol.34
, pp. 49-68
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
5
-
-
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: 2107-17.
-
(1995)
Protein Sci
, vol.4
, pp. 2107-2117
-
-
Godzik, A.1
Kolinski, A.2
Skolnick, J.3
-
6
-
-
0025341310
-
Calculation of conformational ensembles from potentials of mean force
-
Sippl MJ. Calculation of conformational ensembles from potentials of mean force. J Mol Biol 1990;213:859-83.
-
(1990)
J Mol Biol
, vol.213
, pp. 859-883
-
-
Sippl, M.J.1
-
7
-
-
0029000696
-
Knowledge-based potentials for proteins
-
Sippl MJ. Knowledge-based potentials for proteins. Curr Opin Struct Biol 1995;5:229-35.
-
(1995)
Curr Opin Struct Biol
, vol.5
, pp. 229-235
-
-
Sippl, M.J.1
-
8
-
-
0038060686
-
Anisotropic coarse-grained statistical potentials improve the ability to identify native-like protein structures
-
Buchete N-V, Straub JE, Thirumalai D. Anisotropic coarse-grained statistical potentials improve the ability to identify native-like protein structures. J Chem Phys 2003;118:7658-71.
-
(2003)
J Chem Phys
, vol.118
, pp. 7658-7671
-
-
Buchete, N.-V.1
Straub, J.E.2
Thirumalai, D.3
-
9
-
-
0033853177
-
Decoys 'R' Us: A database of incorrect conformations to improve protein structure prediction
-
Samudrala R, Levitt M. Decoys 'R' Us: a database of incorrect conformations to improve protein structure prediction. Protein Sci 2000;9:1399-401.
-
(2000)
Protein Sci
, vol.9
, pp. 1399-1401
-
-
Samudrala, R.1
Levitt, M.2
-
10
-
-
0025368288
-
Metastability of the folded states of globular proteins
-
Honeycutt JD, Thirumalai D. Metastability of the folded states of globular proteins. Proc Natl Acad Sci USA 1990;87:3526-9.
-
(1990)
Proc Natl Acad Sci USA
, vol.87
, pp. 3526-3529
-
-
Honeycutt, J.D.1
Thirumalai, D.2
-
11
-
-
0016610491
-
Computer simulation of protein folding
-
Levitt M, Warshel A. Computer simulation of protein folding. Nature 1975;253:694-8.
-
(1975)
Nature
, vol.253
, pp. 694-698
-
-
Levitt, M.1
Warshel, A.2
-
12
-
-
33845377127
-
Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation
-
Miyazawa S, Jernigan RL. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules 1985;18:534-52.
-
(1985)
Macromolecules
, vol.18
, pp. 534-552
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
14
-
-
0033985050
-
Assigning genomic sequences to CATH
-
Pearl FMG, Lee D, Bray JE, Sillitoe I, Todd AE, Harrison AP, Thornton JM, Orengo CA. Assigning genomic sequences to CATH. Nucl Acids Res 2000;28:277-82.
-
(2000)
Nucl Acids Res
, vol.28
, pp. 277-282
-
-
Pearl, F.M.G.1
Lee, D.2
Bray, J.E.3
Sillitoe, I.4
Todd, A.E.5
Harrison, A.P.6
Thornton, J.M.7
Orengo, C.A.8
-
15
-
-
0030832809
-
Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches
-
Bahar I, Kaplan M, Jernigan RL. Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches. Proteins 1997;29:292-308.
-
(1997)
Proteins
, vol.29
, pp. 292-308
-
-
Bahar, I.1
Kaplan, M.2
Jernigan, R.L.3
-
16
-
-
0033566967
-
Evaluation of short-range interactions as secondary structure energies for protein fold and sequence recognition
-
Miyazawa S, Jernigan RL. Evaluation of short-range interactions as secondary structure energies for protein fold and sequence recognition. Proteins 1999;36:347-56.
-
(1999)
Proteins
, vol.36
, pp. 347-356
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
17
-
-
0030324869
-
Coordination geometry of nonbonded residues in globular proteins
-
Bahar I, Jernigan RL. Coordination geometry of nonbonded residues in globular proteins. Fold Des 1996;1:357-70.
-
(1996)
Fold Des
, vol.1
, pp. 357-370
-
-
Bahar, I.1
Jernigan, R.L.2
-
18
-
-
0000095892
-
A united-residue force field for off-lattice protein-structure simulations. I. Functional forms and parameters of long-range side-chain interaction potentials from protein crystal data
-
Liwo A, Oldziej S, Pincus MR, Wawak RJ, Rackovsky S, Scheraga HA. A united-residue force field for off-lattice protein-structure simulations. I. Functional forms and parameters of long-range side-chain interaction potentials from protein crystal data. J Comput Chem 1997;18:849-73.
-
(1997)
J Comput Chem
, vol.18
, pp. 849-873
-
-
Liwo, A.1
Oldziej, S.2
Pincus, M.R.3
Wawak, R.J.4
Rackovsky, S.5
Scheraga, H.A.6
-
19
-
-
0000095890
-
A united-residue force field for off-lattice protein-structure simulations. I. Parameterization of short-range interactions and determination of weights of energy terms by Z-score optimization
-
Liwo A, Pincus MR, Wawak RJ, Rackovsky S, Oldziej S, Scheraga HA. A united-residue force field for off-lattice protein-structure simulations. I. Parameterization of short-range interactions and determination of weights of energy terms by Z-score optimization. J Comput Chem 1997;18:874-87.
-
(1997)
J Comput Chem
, vol.18
, pp. 874-887
-
-
Liwo, A.1
Pincus, M.R.2
Wawak, R.J.3
Rackovsky, S.4
Oldziej, S.5
Scheraga, H.A.6
-
20
-
-
0001181898
-
United-residue force field for off-lattice protein-structure simulations: III of backbone hydrogen-bonding cooperativity in united-residue potentials
-
Liwo A, Kazmierkiewicz R, Czaplewski C, Groth M, Oldziej S, Wawak RJ, Rackovsky S, Pincus MR, Scheraga HA. United-residue force field for off-lattice protein-structure simulations: III of backbone hydrogen-bonding cooperativity in united-residue potentials. J Comput Chem 1998;19:259-76.
-
(1998)
J Comput Chem
, vol.19
, pp. 259-276
-
-
Liwo, A.1
Kazmierkiewicz, R.2
Czaplewski, C.3
Groth, M.4
Oldziej, S.5
Wawak, R.J.6
Rackovsky, S.7
Pincus, M.R.8
Scheraga, H.A.9
-
21
-
-
0025008445
-
Identification of native protein folds amongst a large number of incorrect models: The calculation of low energy conformations from potentials of mean force
-
Hendlich M, Lackner P, Weitckus S, Floeckner H, Froschauer R, Gottsbacher K, Casari G, Sippl MJ. Identification of native protein folds amongst a large number of incorrect models: the calculation of low energy conformations from potentials of mean force. J Mol Biol 1990;216:167-80.
-
(1990)
J Mol Biol
, vol.216
, pp. 167-180
-
-
Hendlich, M.1
Lackner, P.2
Weitckus, S.3
Floeckner, H.4
Froschauer, R.5
Gottsbacher, K.6
Casari, G.7
Sippl, M.J.8
-
22
-
-
0029976427
-
Statistical potentials extracted from protein structures: How accurate are they?
-
Thomas PD, Dill KA. Statistical potentials extracted from protein structures: how accurate are they? J Mol Biol 1996;257:457-69.
-
(1996)
J Mol Biol
, vol.257
, pp. 457-469
-
-
Thomas, P.D.1
Dill, K.A.2
-
23
-
-
0031585984
-
Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
-
Simons KT, Kooperberg C, Huang ES, Baker D. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 1997; 268:209-25.
-
(1997)
J Mol Biol
, vol.268
, pp. 209-225
-
-
Simons, K.T.1
Kooperberg, C.2
Huang, E.S.3
Baker, D.4
-
24
-
-
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
-
25
-
-
0031566950
-
Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation
-
Bahar I, Jernigan RL. Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation. J Mol Biol 1997;266:195-214.
-
(1997)
J Mol Biol
, vol.266
, pp. 195-214
-
-
Bahar, I.1
Jernigan, R.L.2
-
27
-
-
0032728652
-
Spherepack 3.0: A model development facility
-
Adams JC, Swarztrauber PN, Spherepack 3.0: a model development facility. Monthly Weather Rev 1999;127:1872-8.
-
(1999)
Monthly Weather Rev
, vol.127
, pp. 1872-1878
-
-
Adams, J.C.1
Swarztrauber, P.N.2
-
29
-
-
0038708222
-
A novel approach to decoy set generation: Designing a physical energy function having local minima with native structure characteristics
-
Keasar C, Levitt M. A novel approach to decoy set generation: designing a physical energy function having local minima with native structure characteristics. J Mol Biol 2003;329:159-74.
-
(2003)
J Mol Biol
, vol.329
, pp. 159-174
-
-
Keasar, C.1
Levitt, M.2
-
30
-
-
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: 367-92.
-
(1996)
J Mol Biol
, vol.258
, pp. 367-392
-
-
Park, B.1
Levitt, M.2
-
31
-
-
0031557390
-
Factors affecting the ability of energy functions to discriminate correct from incorrect folds
-
Park B, Huang ES, Levitt M. Factors affecting the ability of energy functions to discriminate correct from incorrect folds. J Mol Biol 1997;266:831-46.
-
(1997)
J Mol Biol
, vol.266
, pp. 831-846
-
-
Park, B.1
Huang, E.S.2
Levitt, M.3
-
32
-
-
0035327508
-
Determination of optimal Chebyshev-expanded hydrophobic discrimination function for globular proteins, IBM
-
Fain B, Xia Y, Levitt M. Determination of optimal Chebyshev-expanded hydrophobic discrimination function for globular proteins, IBM. J Res Dev 2001;45:525-32.
-
(2001)
J Res Dev
, vol.45
, pp. 525-532
-
-
Fain, B.1
Xia, Y.2
Levitt, M.3
-
33
-
-
0033005899
-
Pair potentials for protein folding: Choice of reference states and sensitivity of predicted native states to variations in the interaction schemes
-
Betancourt MR, Thirumalai D. Pair potentials for protein folding: choice of reference states and sensitivity of predicted native states to variations in the interaction schemes. Protein Sci 1999;8:361-9.
-
(1999)
Protein Sci
, vol.8
, pp. 361-369
-
-
Betancourt, M.R.1
Thirumalai, D.2
-
35
-
-
0035826446
-
Hydrophobicity in a simple model of water: Entropy penalty as a sum of competing terms via full, angular expansion
-
Silverstein KAT, Dill KA, Haymet ADJ. Hydrophobicity in a simple model of water: entropy penalty as a sum of competing terms via full, angular expansion. J Chem Phys 2001;114:6303-14.
-
(2001)
J Chem Phys
, vol.114
, pp. 6303-6314
-
-
Silverstein, K.A.T.1
Dill, K.A.2
Haymet, A.D.J.3
-
36
-
-
33748667337
-
Soft sticky dipole potential for liquid water: A new model
-
Liu Y, Ichiye T, Soft sticky dipole potential for liquid water: a new model. J Phys Chem 1996;100:2723-30.
-
(1996)
J Phys Chem
, vol.100
, pp. 2723-2730
-
-
Liu, Y.1
Ichiye, T.2
-
37
-
-
0001064010
-
Dynamical properties of the soft sticky dipole model of water: Molecular dynamics simulations
-
Chandra A, Ichiye T. Dynamical properties of the soft sticky dipole model of water: molecular dynamics simulations. J Phys Chem 1999; 111:2701-9.
-
(1999)
J Phys Chem
, vol.111
, pp. 2701-2709
-
-
Chandra, A.1
Ichiye, T.2
-
38
-
-
0037274128
-
Application of statistical physics to understanding static and dynamic anomalies in liquid water
-
Stanley HE, Buldyrev SV, Giovambattista N, Nave EL, Mossa S, Scala A, Sciortino F, Starr FW, Yamada M. Application of statistical physics to understanding static and dynamic anomalies in liquid water. J Stat Phys 2003;110:1039-54.
-
(2003)
J Stat Phys
, vol.110
, pp. 1039-1054
-
-
Stanley, H.E.1
Buldyrev, S.V.2
Giovambattista, N.3
Nave, E.L.4
Mossa, S.5
Scala, A.6
Sciortino, F.7
Starr, F.W.8
Yamada, M.9
-
41
-
-
0034317110
-
A high-quality X-ray scattering experiment on liquid water at ambient conditions
-
Hura G, Sorenson JM, Glaeser RM. Head-Gordon T. A high-quality X-ray scattering experiment on liquid water at ambient conditions. J Chem Phys 2000;113:9140-8.
-
(2000)
J Chem Phys
, vol.113
, pp. 9140-9148
-
-
Hura, G.1
Sorenson, J.M.2
Glaeser, R.M.3
Head-Gordon, T.4
-
42
-
-
0034316640
-
What can X-ray scattering tell us about the radial distribution functions of water?
-
Sorenson JM, Hura G, Glaeser RM, Head-Gordon T. What can X-ray scattering tell us about the radial distribution functions of water? J Chem Phys 2000;113:9149-61.
-
(2000)
J Chem Phys
, vol.113
, pp. 9149-9161
-
-
Sorenson, J.M.1
Hura, G.2
Glaeser, R.M.3
Head-Gordon, T.4
-
43
-
-
0000020246
-
A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions
-
Mahoney MW, Jorgensen WL. A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions. J Chem Phys 2000;112:8910-22.
-
(2000)
J Chem Phys
, vol.112
, pp. 8910-8922
-
-
Mahoney, M.W.1
Jorgensen, W.L.2
-
44
-
-
0042415783
-
NAMD2: Greater scalability for parallel molecular dynamics
-
Kale L, Skeel R, Bhandarkar M, Brunner R, A G, Krawetz N, Phillips J, Shinozaki A, Varadarajan K, Schulten K. NAMD2: greater scalability for parallel molecular dynamics. J Comput Phys 1999; 151:283-312.
-
(1999)
J Comput Phys
, vol.151
, pp. 283-312
-
-
Kale, L.1
Skeel, R.2
Bhandarkar, M.3
Brunner, R.A.G.4
Krawetz, N.5
Phillips, J.6
Shinozaki, A.7
Varadarajan, K.8
Schulten, K.9
|