-
1
-
-
0002638513
-
The protein databank
-
Bonn, Cambridge and Chester: Data Commission of the International Union of Crystallography
-
Abola E. E., Bernstein F. C., Bryant S. H., Koetzle T. F., Weng J. The protein databank. In Crystallographic Databases-Information Content Software Systems, Scientific Applications. 1987;Data Commission of the International Union of Crystallography, Bonn, Cambridge and Chester.
-
(1987)
Crystallographic Databases-Information Content Software Systems, Scientific Applications
-
-
Abola, E.E.1
Bernstein, F.C.2
Bryant, S.H.3
Koetzle, T.F.4
Weng, J.5
-
2
-
-
0030324869
-
Coordination geometry of non-bonded residues in globular proteins
-
Bahar I., Jernigan R. L. Coordination geometry of non-bonded residues in globular proteins. Folding Des. 1:1996;357-370.
-
(1996)
Folding Des.
, vol.1
, pp. 357-370
-
-
Bahar, I.1
Jernigan, R.L.2
-
4
-
-
0017411710
-
The protein databank: A computer-based archival file for macromolecular structures
-
Bernstein F., Koetzel T., Williams G., Meyer E., Brice M., Rodgers J., Kennard O., Shimanouchi T., Tasumi M. The protein databank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112:1977;535-542.
-
(1977)
J. Mol. Biol.
, vol.112
, pp. 535-542
-
-
Bernstein, F.1
Koetzel, T.2
Williams, G.3
Meyer, E.4
Brice, M.5
Rodgers, J.6
Kennard, O.7
Shimanouchi, T.8
Tasumi, M.9
-
5
-
-
0025830469
-
A method to identify protein sequences that fold into a known 3-dimensional structure
-
Bowie J. U., Lüthy R., Eisenberg D. A method to identify protein sequences that fold into a known 3-dimensional structure. Science. 253:1991;164-170.
-
(1991)
Science
, vol.253
, pp. 164-170
-
-
Bowie, J.U.1
Lüthy, R.2
Eisenberg, D.3
-
6
-
-
0000050840
-
The configuration of random polypeptide theory
-
Brant D. A., Flory P. J. The configuration of random polypeptide theory. J. Am. Chem. Soc. 87:1965;2791-2800.
-
(1965)
J. Am. Chem. Soc.
, vol.87
, pp. 2791-2800
-
-
Brant, D.A.1
Flory, P.J.2
-
7
-
-
0028351287
-
An improved pair potential to recognize native protein folds
-
Brauer A., Beyer A. An improved pair potential to recognize native protein folds. Proteins: Struct. Funct. Genet. 18:1994;254-261.
-
(1994)
Proteins: Struct. Funct. Genet.
, vol.18
, pp. 254-261
-
-
Brauer, A.1
Beyer, A.2
-
8
-
-
0027318317
-
An empirical energy function for threading protein sequence through the folding motif
-
Bryant S. H., Lawrence C. E. An empirical energy function for threading protein sequence through the folding motif. Proteins: Struct. Funct. Genet. 16:1993;92-112.
-
(1993)
Proteins: Struct. Funct. Genet.
, vol.16
, pp. 92-112
-
-
Bryant, S.H.1
Lawrence, C.E.2
-
9
-
-
0024260626
-
Weakly polar interactions in proteins
-
Burley S. K., Petsko G. A. Weakly polar interactions in proteins. Advan. Protein Chem. 39:1988;125-189.
-
(1988)
Advan. Protein Chem.
, vol.39
, pp. 125-189
-
-
Burley, S.K.1
Petsko, G.A.2
-
10
-
-
0026539511
-
Structure-derived hydrophobic potential. Hydrophobic potential derived from X-ray structures of globular proteins is able to identify native folds
-
Casari G., Sippl M. J. Structure-derived hydrophobic potential. Hydrophobic potential derived from X-ray structures of globular proteins is able to identify native folds. J. Mol. Biol. 244:1992;725-732.
-
(1992)
J. Mol. Biol.
, vol.244
, pp. 725-732
-
-
Casari, G.1
Sippl, M.J.2
-
11
-
-
0023645034
-
Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins
-
Cornette J. L., Cease K. B., Margalit H., Spouge J. L., Berzofsky J. A., Delisi C. Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins. J. Mol. Biol. 195:1987;659-685.
-
(1987)
J. Mol. Biol.
, vol.195
, pp. 659-685
-
-
Cornette, J.L.1
Cease, K.B.2
Margalit, H.3
Spouge, J.L.4
Berzofsky, J.A.5
Delisi, C.6
-
12
-
-
0025319917
-
Conformations of folded proteins in restricted spaces
-
Covell D. G., Jernigan R. L. Conformations of folded proteins in restricted spaces. Biochemistry. 29:1990;3287-3294.
-
(1990)
Biochemistry
, vol.29
, pp. 3287-3294
-
-
Covell, D.G.1
Jernigan, R.L.2
-
13
-
-
0022070389
-
Sidechain and backbone potential functions for conformational analysis of proteins
-
Crippen G. M., Viswanadhan N. V. Sidechain and backbone potential functions for conformational analysis of proteins. Int. J. Pept. Protein Res. 25:1985;487-509.
-
(1985)
Int. J. Pept. Protein Res.
, vol.25
, pp. 487-509
-
-
Crippen, G.M.1
Viswanadhan, N.V.2
-
14
-
-
0028153795
-
Planar stacking interactions of arginine and aromatic side-chains in proteins
-
Flocco M. M., Mowbray S. L. Planar stacking interactions of arginine and aromatic side-chains in proteins. J. Mol. Biol. 235:1994;709-717.
-
(1994)
J. Mol. Biol.
, vol.235
, pp. 709-717
-
-
Flocco, M.M.1
Mowbray, S.L.2
-
15
-
-
0027050011
-
Sequence-structure matching in globular proteins. Applications to supersecondary and tertiary structure determination
-
Godzik A., Skolnick J. Sequence-structure matching in globular proteins. Applications to supersecondary and tertiary structure determination. Proc. Natl Acad. Sci. USA. 89:1992;98-102.
-
(1992)
Proc. Natl Acad. Sci. USA
, vol.89
, pp. 98-102
-
-
Godzik, A.1
Skolnick, J.2
-
16
-
-
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. 4:1995;2107-2117.
-
(1995)
Protein Sci.
, vol.4
, pp. 2107-2117
-
-
Godzik, A.1
Kolinski, A.2
Skolnick, J.3
-
17
-
-
0026716018
-
Effects of compact volume and chain stiffness on the conformations of native proteins
-
Hao M., Rackovsky S., Liwo A., Pincus M. R., Scheraga H. A. Effects of compact volume and chain stiffness on the conformations of native proteins. Proc. Natl Acad. Sci. USA. 89:1992;6614-6618.
-
(1992)
Proc. Natl Acad. Sci. USA
, vol.89
, pp. 6614-6618
-
-
Hao, M.1
Rackovsky, S.2
Liwo, A.3
Pincus, M.R.4
Scheraga, H.A.5
-
18
-
-
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 M. J. 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. 216:1990;167-180.
-
(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
-
19
-
-
0028205447
-
Enlarged representative set of protein structures
-
Hobohm U., Sander C. Enlarged representative set of protein structures. Protein Sci. 3:1994;522-524.
-
(1994)
Protein Sci.
, vol.3
, pp. 522-524
-
-
Hobohm, U.1
Sander, C.2
-
22
-
-
0029942661
-
Simple empirical potentials derived from structures and their use in protein simulations
-
Jernigan R. L., Bahar I. Simple empirical potentials derived from structures and their use in 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
-
23
-
-
0026690571
-
A new approach to protein fold recognition
-
Jones D. T., Taylor W. R., Thornton J. M. A new approach to protein fold recognition. Nature. 358:1992;86-89.
-
(1992)
Nature
, vol.358
, pp. 86-89
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
24
-
-
0028318094
-
Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches
-
Kocher J.-P. A., Rooman M. J., Wodak S. Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches. J. Mol. Biol. 235:1994;1598-1613.
-
(1994)
J. Mol. Biol.
, vol.235
, pp. 1598-1613
-
-
Kocher, J.-P.A.1
Rooman, M.J.2
Wodak, S.3
-
25
-
-
0017157584
-
A simplified representation of protein conformations for rapid simulation of protein folding
-
Levitt M. A simplified representation of protein conformations for rapid simulation of protein folding. J. Mol. Biol. 104:1976;59-107.
-
(1976)
J. Mol. Biol.
, vol.104
, pp. 59-107
-
-
Levitt, M.1
-
26
-
-
0024292833
-
Aromatic rings act as hydrogen bond acceptors
-
Levitt M., Perutz M. F. Aromatic rings act as hydrogen bond acceptors. J. Mol. Biol. 201:1988;751-754.
-
(1988)
J. Mol. Biol.
, vol.201
, pp. 751-754
-
-
Levitt, M.1
Perutz, M.F.2
-
27
-
-
0016610491
-
Computer simulation of protein folding
-
Levitt M., Warshel A. Computer simulation of protein folding. Nature. 253:1975;694-698.
-
(1975)
Nature
, vol.253
, pp. 694-698
-
-
Levitt, M.1
Warshel, A.2
-
28
-
-
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
-
29
-
-
0001469314
-
Empirical studies of hydrophobicity. 1. Effect of protein size and the hydrophobic behavior of amino acids
-
Meirovitch H., Rackovsky S., Scheraga H A. Empirical studies of hydrophobicity. 1. Effect of protein size and the hydrophobic behavior of amino acids. Macromolecules. 13:1980;1398-1405.
-
(1980)
Macromolecules
, vol.13
, pp. 1398-1405
-
-
Meirovitch, H.1
Rackovsky, S.2
Scheraga, H.A.3
-
30
-
-
0028301445
-
Amino-aromatic interactions in proteins: Is the evidence stacked against hydrogen bonding?
-
Mitchell J. B. O., Nandi C. L., McDonald I. K., Thornton J. M., Price S. Amino-aromatic interactions in proteins: is the evidence stacked against hydrogen bonding? J. Mol. Biol. 239:1994;315-331.
-
(1994)
J. Mol. Biol.
, vol.239
, pp. 315-331
-
-
Mitchell, J.B.O.1
Nandi, C.L.2
McDonald, I.K.3
Thornton, J.M.4
Price, S.5
-
31
-
-
33845377127
-
Estimation of effective inter-residue contact energies from protein crystal structures: Quasi-chemical approximation
-
Miyazawa S., Jernigan R. L. Estimation of effective inter-residue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules. 18:1985;534-552.
-
(1985)
Macromolecules
, vol.18
, pp. 534-552
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
32
-
-
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
-
33
-
-
0028897718
-
Computer modeling of protein folding: Conformational and energetic analysis of reduced and detailed protein models
-
Monge A., Lathrop E. J., Gunn J. R., Shenkin R. S., Friesner R. A. Computer modeling of protein folding: conformational and energetic analysis of reduced and detailed protein models. J. Mol. Biol. 247:1995;995-1012.
-
(1995)
J. Mol. Biol.
, vol.247
, pp. 995-1012
-
-
Monge, A.1
Lathrop, E.J.2
Gunn, J.R.3
Shenkin, R.S.4
Friesner, R.A.5
-
34
-
-
0015217634
-
The solubility of amino acids and two glycine peptide in aqueous ethanol and dioxane solutions. Establishment of hydrophobicity scales
-
Nozaki Y., Tanford C. The solubility of amino acids and two glycine peptide in aqueous ethanol and dioxane solutions. Establishment of hydrophobicity scales. J. Biol. Chem. 246:1971;2211.
-
(1971)
J. Biol. Chem.
, vol.246
, pp. 2211
-
-
Nozaki, Y.1
Tanford, C.2
-
35
-
-
0029987862
-
Energy functions that discriminate X-ray and near-native folds from well-constructed decoys
-
Park B. H., 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.H.1
Levitt, M.2
-
36
-
-
0019163107
-
Spatial assignment of amino acid residues in globular proteins: An approach from information theory
-
Prabhakaran M., Ponnuswamy P. K. Spatial assignment of amino acid residues in globular proteins: an approach from information theory. J. Theor. Biol. 87:1980;623-637.
-
(1980)
J. Theor. Biol.
, vol.87
, pp. 623-637
-
-
Prabhakaran, M.1
Ponnuswamy, P.K.2
-
37
-
-
0022412192
-
Hydrophobicity of amino acid residues in globular proteins
-
Rose G., Geselowitz A., Lesser G., Lee R., Zehfus M. Hydrophobicity of amino acid residues in globular proteins. Science. 229:1985;834-838.
-
(1985)
Science
, vol.229
, pp. 834-838
-
-
Rose, G.1
Geselowitz, A.2
Lesser, G.3
Lee, R.4
Zehfus, M.5
-
38
-
-
0027291015
-
Prediction of protein secondary structure at better than 70% accuracy
-
Rost B., Sander C. Prediction of protein secondary structure at better than 70% accuracy. J. Mol. Biol. 232:1993;584-589.
-
(1993)
J. Mol. Biol.
, vol.232
, pp. 584-589
-
-
Rost, B.1
Sander, C.2
-
39
-
-
0025341310
-
Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins
-
Sippl M. 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. 213:1990;859-883.
-
(1990)
J. Mol. Biol.
, vol.213
, pp. 859-883
-
-
Sippl, M.1
-
41
-
-
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. 2:1993;762-785.
-
(1993)
Protein Sci.
, vol.2
, pp. 762-785
-
-
Sun, S.1
-
42
-
-
0026650809
-
Protein structure prediction based on statistical potential
-
Sun S., Luo N., Ornstein R., Rein R. Protein structure prediction based on statistical potential. Biophys. J. 62:1992;104-106.
-
(1992)
Biophys. J.
, vol.62
, pp. 104-106
-
-
Sun, S.1
Luo, N.2
Ornstein, R.3
Rein, R.4
-
43
-
-
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
-
44
-
-
0028347939
-
A simplified amino acid potential for use in structure predictions of proteins
-
Wallqvist A., Ullner M. A simplified amino acid potential for use in structure predictions of proteins. Proteins: Struct. Funct. Genet. 18:1994;267-280.
-
(1994)
Proteins: Struct. Funct. Genet.
, vol.18
, pp. 267-280
-
-
Wallqvist, A.1
Ullner, M.2
-
45
-
-
0029119320
-
A preference-based free energy parameterization of enzyme-inhibitor binding. Applications to HIV-1-protease inhibitor design
-
Wallqvist A., Jernigan R. L., Covell D. G. A preference-based free energy parameterization of enzyme-inhibitor binding. Applications to HIV-1-protease inhibitor design. Protein Sci. 4:1995;1881-1903.
-
(1995)
Protein Sci
, vol.4
, pp. 1881-1903
-
-
Wallqvist, A.1
Jernigan, R.L.2
Covell, D.G.3
-
46
-
-
0028895567
-
Discriminating compact nonnative structures from the native structure of globular proteins
-
Wang Y., Zhang H., Li W., Scott R. A. Discriminating compact nonnative structures from the native structure of globular proteins. Proc. Natl Acad. Sci. USA. 92:1995a;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
-
47
-
-
0029077858
-
A new computational model for protein folding based on atomic solvation
-
Wang Y., Zhang H., Scott R. A. A new computational model for protein folding based on atomic solvation. Protein Sci. 4:1995b;1402-1411.
-
(1995)
Protein Sci.
, vol.4
, pp. 1402-1411
-
-
Wang, Y.1
Zhang, H.2
Scott, R.A.3
-
48
-
-
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: Struct. Funct. Genet. 6:1989;193-209.
-
(1989)
Proteins: Struct. Funct. Genet.
, vol.6
, pp. 193-209
-
-
Wilson, C.1
Doniach, S.2
|