-
1
-
-
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;18:534-552.
-
(1985)
Macromolecules
, vol.18
, pp. 534-552
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
2
-
-
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
-
3
-
-
0026519315
-
A lattice model for protein structure prediction at low resolution
-
Hinds DA, Levitt M. A lattice model for protein structure prediction at low resolution. Proc Natl Acad Sci USA 1992;89:2536-2540.
-
(1992)
Proc Natl Acad Sci USA
, vol.89
, pp. 2536-2540
-
-
Hinds, D.A.1
Levitt, M.2
-
4
-
-
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
-
5
-
-
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;213:859-883.
-
(1990)
J Mol Biol
, vol.213
, pp. 859-883
-
-
Sippl, M.J.1
-
6
-
-
0027318317
-
An empirical energy function for threading protein sequence through the folding motif
-
Bryant SH, Lawrence CE. An empirical energy function for threading protein sequence through the folding motif. Proteins 1993;16:92-112.
-
(1993)
Proteins
, vol.16
, pp. 92-112
-
-
Bryant, S.H.1
Lawrence, C.E.2
-
7
-
-
0028075953
-
Protein stability for single substitution mutants and the extent of local compactness in the denatured state
-
Miyazawa S, Jernigan RL. Protein stability for single substitution mutants and the extent of local compactness in the denatured state. Protein Eng 1994;7:1209-1220.
-
(1994)
Protein Eng
, vol.7
, pp. 1209-1220
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
8
-
-
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, Floechner H, Froschauer R, Gottsbachner 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;216:167-180.
-
(1990)
J Mol Biol
, vol.216
, pp. 167-180
-
-
Hendlich, M.1
Lackner, P.2
Weitckus, S.3
Floechner, H.4
Froschauer, R.5
Gottsbachner, K.6
Casari, G.7
Sippl, M.J.8
-
9
-
-
0026704815
-
Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a data base of known protein conformations
-
Sippl MJ, Weitckus S. Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a data base of known protein conformations. Proteins 1992;13:258-271.
-
(1992)
Proteins
, vol.13
, pp. 258-271
-
-
Sippl, M.J.1
Weitckus, S.2
-
10
-
-
0026690571
-
A new approach to protein fold recognition
-
Jones DT, Taylor WR, Thornton JM. A new approach to protein fold recognition. Nature 1992;358:86-89.
-
(1992)
Nature
, vol.358
, pp. 86-89
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
11
-
-
0027050011
-
Sequence-structure matching in globular proteins: Application to super-secondary and tertiary structure determination
-
Godzik A, Skolnick J. Sequence-structure matching in globular proteins: Application to super-secondary and tertiary structure determination. Proc Natl Acad Sci USA 1992;89:12098-12102.
-
(1992)
Proc Natl Acad Sci USA
, vol.89
, pp. 12098-12102
-
-
Godzik, A.1
Skolnick, J.2
-
12
-
-
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
-
14
-
-
0028892389
-
Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets
-
Godzik A, Koliński 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
Koliński, A.2
Skolnick, J.3
-
15
-
-
0025830469
-
A method to identify protein sequences that fold into a known three-dimensional structure
-
Bowie JU, Lüthy R, Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science 1991;253:164-170.
-
(1991)
Science
, vol.253
, pp. 164-170
-
-
Bowie, J.U.1
Lüthy, R.2
Eisenberg, D.3
-
16
-
-
0027504808
-
Development of pseudoenergy potentials for assessing protein 3-D-1-D compatibility and detecting weak homologies
-
Nishikawa K, Matsuo Y. Development of pseudoenergy potentials for assessing protein 3-D-1-D compatibility and detecting weak homologies. Protein Eng 1993;6:811-820.
-
(1993)
Protein Eng
, vol.6
, pp. 811-820
-
-
Nishikawa, K.1
Matsuo, Y.2
-
17
-
-
0029083544
-
Detection of protein 3D-1D compatibility characterized by the evaluation of side-chain packing and electrostatic interactions
-
Matsuo Y, Nakamura H, Nishikawa K. Detection of protein 3D-1D compatibility characterized by the evaluation of side-chain packing and electrostatic interactions. J Biochem (Tokyo) 1995;118:137-148.
-
(1995)
J Biochem (Tokyo)
, vol.118
, pp. 137-148
-
-
Matsuo, Y.1
Nakamura, H.2
Nishikawa, K.3
-
18
-
-
0026610767
-
Assessment of protein models with three-dimensional profiles
-
Lüthy R, Bowie JU, Eisenberg D. Assessment of protein models with three-dimensional profiles. Nature 1992;356:83-85.
-
(1992)
Nature
, vol.356
, pp. 83-85
-
-
Lüthy, R.1
Bowie, J.U.2
Eisenberg, D.3
-
19
-
-
0027516008
-
Computer simulation of antibody binding specificity
-
Pellegrini M, Doniach S. Computer simulation of antibody binding specificity. Proteins 1993;15:436-444.
-
(1993)
Proteins
, vol.15
, pp. 436-444
-
-
Pellegrini, M.1
Doniach, S.2
-
20
-
-
0029018773
-
Ranking potential binding peptides to MHC molecules by a computational threading approach
-
Altuvia Y, Schueler O, Margalit H. Ranking potential binding peptides to MHC molecules by a computational threading approach. J Mol Biol 1995;249:244-250.
-
(1995)
J Mol Biol
, vol.249
, pp. 244-250
-
-
Altuvia, Y.1
Schueler, O.2
Margalit, H.3
-
21
-
-
0029119320
-
A preference-based free-energy parameterization of enzyme-inhibitor binding. Applications to HIV-1-protease inhibitor design
-
Wallqvist A, Jernigan RL, Covell DG. A preference-based free-energy parameterization of enzyme-inhibitor binding. Applications to HIV-1-protease inhibitor design. Protein Sci 1995;4:1881-1903.
-
(1995)
Protein Sci
, vol.4
, pp. 1881-1903
-
-
Wallqvist, A.1
Jernigan, R.L.2
Covell, D.G.3
-
22
-
-
0024435638
-
A computer model to dynamically simulate protein folding: Studies with crambin
-
Wilson C, Doniach S. A computer model to dynamically simulate protein folding: Studies with crambin. Proteins 1989;6:193-209.
-
(1989)
Proteins
, vol.6
, pp. 193-209
-
-
Wilson, C.1
Doniach, S.2
-
23
-
-
0025608908
-
Simulations of folding of a globular proteins
-
Skolnick J, Kolinski A. Simulations of folding of a globular proteins. Science 1990;250:1121-1125.
-
(1990)
Science
, vol.250
, pp. 1121-1125
-
-
Skolnick, J.1
Kolinski, A.2
-
24
-
-
0027503403
-
Reduced representation model of protein structure prediction: Statistical potential and genetic algorithms
-
Sun S. Reduced representation model of protein structure prediction: Statistical potential and genetic algorithms. Protein Sci 1993;2:762-785.
-
(1993)
Protein Sci
, vol.2
, pp. 762-785
-
-
Sun, S.1
-
25
-
-
0028203492
-
Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme
-
Koliński A, Skolnick J. Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme. Proteins 1994;18:338-352.
-
(1994)
Proteins
, vol.18
, pp. 338-352
-
-
Koliński, A.1
Skolnick, J.2
-
27
-
-
0015244817
-
Empirical protein energy maps
-
Pohl FM. Empirical protein energy maps. Nature New Biol 1971;234:277-279.
-
(1971)
Nature New Biol
, vol.234
, pp. 277-279
-
-
Pohl, F.M.1
-
28
-
-
0345483175
-
Statistical analysis of protein structures
-
Jaenieke R, editor. Amsterdam: Elsevier/North-Holland Biomedical Press
-
Pohl FM. Statistical analysis of protein structures. In: Jaenieke R, editor. Protein Folding. Amsterdam: Elsevier/North-Holland Biomedical Press; 1980. p 183-196.
-
(1980)
Protein Folding
, pp. 183-196
-
-
Pohl, F.M.1
-
30
-
-
0026016378
-
The frequency of ion-pair substructures in proteins is quantitatively related to electrostatic potential: A statistical model for nonbonded interactions
-
Bryant S, Lawrence CE. The frequency of ion-pair substructures in proteins is quantitatively related to electrostatic potential: A statistical model for nonbonded interactions. Proteins 1991;9:108-119.
-
(1991)
Proteins
, vol.9
, pp. 108-119
-
-
Bryant, S.1
Lawrence, C.E.2
-
31
-
-
0025890946
-
Influence of proline residues on protein formation
-
MacArthur MW, Thornton JM. Influence of proline residues on protein formation. J Mol Biol 1991;218:397-412.
-
(1991)
J Mol Biol
, vol.218
, pp. 397-412
-
-
MacArthur, M.W.1
Thornton, J.M.2
-
32
-
-
0023051843
-
Internal cavities and buried waters in globular proteins
-
Rashin AA, Ionif M, Honig B. Internal cavities and buried waters in globular proteins. Biochemistry 1986;25:3619-3625.
-
(1986)
Biochemistry
, vol.25
, pp. 3619-3625
-
-
Rashin, A.A.1
Ionif, M.2
Honig, B.3
-
33
-
-
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;257:457-469.
-
(1996)
J Mol Biol
, vol.257
, pp. 457-469
-
-
Thomas, P.D.1
Dill, K.A.2
-
34
-
-
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
-
35
-
-
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
-
37
-
-
0017411710
-
The protein data bank: A computer-based archival file for macromolecular structures
-
Bernstein FC, Koetzle TF, Williams GJB et al. The protein data bank: A computer-based archival file for macromolecular structures. J Mol Biol 1977;112:535-542.
-
(1977)
J Mol Biol
, vol.112
, pp. 535-542
-
-
Bernstein, F.C.1
Koetzle, T.F.2
Williams, G.J.B.3
-
38
-
-
0030850226
-
Ideal architecture of residues packing and its observation in protein structures
-
Raghunathan G, Jernigan RL. Ideal architecture of residues packing and its observation in protein structures. Protein Sci 1997;6:2072-2083.
-
(1997)
Protein Sci
, vol.6
, pp. 2072-2083
-
-
Raghunathan, G.1
Jernigan, R.L.2
-
39
-
-
0015217634
-
The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxane solutions; establishment of hydrophobicity scale
-
Nozaki Y, Tanford C. The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxane solutions; establishment of hydrophobicity scale. J Biol Chem 1971;246:2211-2217.
-
(1971)
J Biol Chem
, vol.246
, pp. 2211-2217
-
-
Nozaki, Y.1
Tanford, C.2
-
40
-
-
0028961335
-
Scop: A structural classification of proteins database for the investigation of sequences and structures
-
Murzin AG, Brenner SE, Hubbard T, Chothia C. Scop: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995;247:536-540.
-
(1995)
J Mol Biol
, vol.247
, pp. 536-540
-
-
Murzin, A.G.1
Brenner, S.E.2
Hubbard, T.3
Chothia, C.4
-
42
-
-
0028801308
-
Why do protein architectures have Boltzmann-like statistics?
-
Finkelstein AV, Badretdinov AYa, Gutin AM. Why do protein architectures have Boltzmann-like statistics? Proteins 1995;23: 142-150.
-
(1995)
Proteins
, vol.23
, pp. 142-150
-
-
Finkelstein, A.V.1
Badretdinov, A.Ya.2
Gutin, A.M.3
-
43
-
-
0030983768
-
Derivation and testing of pair potentials for protein folding. When is the quasi-chemical approximation correct?
-
Skolnick J, Jaroszewski L, Kolinski A, Godzik A. Derivation and testing of pair potentials for protein folding. When is the quasi-chemical 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
-
44
-
-
0030806961
-
Statistical significance of hierarchical multi-body potentials based on Delaunay tessellation and their application in sequence-structure alignment
-
Munson PJ, Singh RK. Statistical significance of hierarchical multi-body potentials based on Delaunay tessellation and their application in sequence-structure alignment. Prot Sci 1997;6:1467-1481.
-
(1997)
Prot Sci
, vol.6
, pp. 1467-1481
-
-
Munson, P.J.1
Singh, R.K.2
-
45
-
-
0027650879
-
Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures
-
Sippl MJ. Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures. J Comput Aided Mol Des. 1993;7:473-501.
-
(1993)
J Comput Aided Mol Des.
, vol.7
, pp. 473-501
-
-
Sippl, M.J.1
-
46
-
-
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, P Lackner S, Witckus H et al. 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;216:167-180.
-
(1990)
J Mol Biol
, vol.216
, pp. 167-180
-
-
Hendlich, M.1
P Lackner, S.2
Witckus, H.3
|