-
1
-
-
0017411710
-
Protein Data Bank: A computer-based archival file for macromolecular structures
-
Bernstein F. C., Koetzle T. F., Williams G. J. B., Meyer E. F., Brice M. D., Jr, Rodgers J. R., Kennard O., Shimanouchi T., Tasumi M. Protein Data Bank: 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.C.1
Koetzle, T.F.2
Williams, G.J.B.3
Meyer, E.F.4
Brice M.D., Jr.5
Rodgers, J.R.6
Kennard, O.7
Shimanouchi, T.8
Tasumi, M.9
-
2
-
-
0028328263
-
An evolutionary approach to folding small alpha-helical proteins that uses sequence information and an empirical guiding fitness function
-
Bowie J. U., Eisenberg D. An evolutionary approach to folding small alpha-helical proteins that uses sequence information and an empirical guiding fitness function. Proc. Natl Acad. Sci. USA, 91:1994;4436-4440.
-
(1994)
Proc. Natl Acad. Sci. USA
, vol.91
, pp. 4436-4440
-
-
Bowie, J.U.1
Eisenberg, D.2
-
3
-
-
0025830469
-
A method to identify protein sequences that fold into a known three-dimensional structure
-
Bowie J. U., Lüthy R., Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science. 253:1991;164-170.
-
(1991)
Science
, vol.253
, pp. 164-170
-
-
Bowie, J.U.1
Lüthy, R.2
Eisenberg, D.3
-
4
-
-
0027318317
-
An empirical energy function for threading protein sequence through folding motif
-
Bryant S. H., Lawrence C. E. An empirical energy function for threading protein sequence through 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
-
5
-
-
0018791941
-
Protein folding: Evaluation of some simple rules for the assembly of helices into tertiary structures with myoglobin as an example
-
Cohen F. E., Richmond T. J., Richards F. M. Protein folding: evaluation of some simple rules for the assembly of helices into tertiary structures with myoglobin as an example. J. Mol. Biol. 132:1979;275-288.
-
(1979)
J. Mol. Biol.
, vol.132
, pp. 275-288
-
-
Cohen, F.E.1
Richmond, T.J.2
Richards, F.M.3
-
6
-
-
0026761547
-
Folding protein α-carbon chains into compact forms by Monte Carlo methods
-
Covell D. G. Folding protein α-carbon chains into compact forms by Monte Carlo methods. Proteins: Struct. Funct. Genet. 14:1992;409-420.
-
(1992)
Proteins: Struct. Funct. Genet.
, vol.14
, pp. 409-420
-
-
Covell, D.G.1
-
7
-
-
0028049306
-
Lattice model simulations of polypeptide chain folding
-
Covell D. G. Lattice model simulations of polypeptide chain folding. J. Mol. Biol. 235:1994;1032-1043.
-
(1994)
J. Mol. Biol.
, vol.235
, pp. 1032-1043
-
-
Covell, D.G.1
-
8
-
-
0028297304
-
Folding the main chain of small proteins with the genetic algorithm
-
Dandekar T., Argos P. Folding the main chain of small proteins with the genetic algorithm. J. Mol. Biol. 236:1994;844-861.
-
(1994)
J. Mol. Biol.
, vol.236
, pp. 844-861
-
-
Dandekar, T.1
Argos, P.2
-
9
-
-
0029980527
-
Identifying the tertiary fold of small proteins with different topologies from sequence and secondary structure using the genetic algorithm and extended criteria specific for strand regions
-
Dandekar T., Argos P. Identifying the tertiary fold of small proteins with different topologies from sequence and secondary structure using the genetic algorithm and extended criteria specific for strand regions. J. Mol. Biol. 256:1996;645-660.
-
(1996)
J. Mol. Biol.
, vol.256
, pp. 645-660
-
-
Dandekar, T.1
Argos, P.2
-
10
-
-
0029874551
-
Protein fold recognition using sequence-derived predictions
-
Fischer D., Eisenberg D. Protein fold recognition using sequence-derived predictions. Protein Sci. 5:1996;947-955.
-
(1996)
Protein Sci.
, vol.5
, pp. 947-955
-
-
Fischer, D.1
Eisenberg, D.2
-
11
-
-
0026726481
-
Topology fingerprint approach to the inverse protein folding problem
-
Godzik A., Kolinski A., Skolnick J. Topology fingerprint approach to the inverse protein folding problem. J. Mol. Biol. 227:1992;227-238.
-
(1992)
J. Mol. Biol.
, vol.227
, pp. 227-238
-
-
Godzik, A.1
Kolinski, A.2
Skolnick, J.3
-
12
-
-
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
-
13
-
-
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
-
14
-
-
0026519315
-
A lattice model for protein structure prediction at low resolution
-
Hinds D. A., Levitt M. A lattice model for protein structure prediction at low resolution. Proc. Natl Acad. Sci. USA. 89:1992;2536-2540.
-
(1992)
Proc. Natl Acad. Sci. USA
, vol.89
, pp. 2536-2540
-
-
Hinds, D.A.1
Levitt, M.2
-
15
-
-
0028149160
-
Exploring conformational space with a simple lattice model for protein structure
-
Hinds D. A., Levitt M. Exploring conformational space with a simple lattice model for protein structure. J. Mol. Biol. 243:1994;668-682.
-
(1994)
J. Mol. Biol.
, vol.243
, pp. 668-682
-
-
Hinds, D.A.1
Levitt, M.2
-
16
-
-
0029101826
-
Recognizing native folds by the arrangement of hydrophobic and polar residues
-
Huang E. S., Subbiah S., Levitt M. Recognizing native folds by the arrangement of hydrophobic and polar residues. J. Mol. Biol. 252:1995;709-720.
-
(1995)
J. Mol. Biol.
, vol.252
, pp. 709-720
-
-
Huang, E.S.1
Subbiah, S.2
Levitt, M.3
-
17
-
-
0029871791
-
Using a hydrophobic contact potential to evaluate native and near-native folds generated by molecular dynamics simulations
-
Huang E. S., 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. 257:1996;716-725.
-
(1996)
J. Mol. Biol.
, vol.257
, pp. 716-725
-
-
Huang, E.S.1
Subbiah, S.2
Tsai, J.3
Levitt, M.4
-
18
-
-
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
-
19
-
-
0028318094
-
Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches
-
Kocher J.-P.A., Rooman M. J., Wodak S. J. 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.J.3
-
20
-
-
0028203492
-
Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme
-
Kolinski A., Skolnick J. Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme. Proteins: Struct. Funct. Genet. 18:1994;338-352.
-
(1994)
Proteins: Struct. Funct. Genet.
, vol.18
, pp. 338-352
-
-
Kolinski, A.1
Skolnick, J.2
-
21
-
-
0021104755
-
Molecular dynamics of native protein. II. Analysis and nature of motion
-
Levitt M. Molecular dynamics of native protein. II. Analysis and nature of motion. J. Mol. Biol. 168:1983;621-657.
-
(1983)
J. Mol. Biol.
, vol.168
, pp. 621-657
-
-
Levitt, M.1
-
22
-
-
0029912991
-
Global optimum protein threading with gapped alignment and empirical pair score functions
-
Lathrop R. H., Smith T. F. Global optimum protein threading with gapped alignment and empirical pair score functions. J. Mol. Biol. 255:1995;641-665.
-
(1995)
J. Mol. Biol.
, vol.255
, pp. 641-665
-
-
Lathrop, R.H.1
Smith, T.F.2
-
23
-
-
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
-
24
-
-
33845377127
-
Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation
-
Miyazawa S., Jernigan R. L. Estimation of effective interresidue 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
-
25
-
-
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
-
26
-
-
0028897718
-
Computer modeling of protein folding: Conformational and energy analysis of reduced and detailed protein models
-
Monge A., Lathrop E. J. P., Gunn J. R., Shenkin P. S., Friesner R. A. Computer modeling of protein folding: conformational and energy 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.P.2
Gunn, J.R.3
Shenkin, P.S.4
Friesner, R.A.5
-
27
-
-
0028955505
-
Predicting the helix packing of globular proteins by sel-correcting distance geometry
-
Mumenthaler C., Braun W. Predicting the helix packing of globular proteins by sel-correcting distance geometry. Protein Sci. 4:1995;863-871.
-
(1995)
Protein Sci.
, vol.4
, pp. 863-871
-
-
Mumenthaler, C.1
Braun, W.2
-
28
-
-
0014757386
-
A general method applicable to the search for similarities in the amino acid sequences of two proteins
-
Needleman S. B., Wunsch C. B. A general method applicable to the search for similarities in the amino acid sequences of two proteins. J. Mol. Biol. 48:1970;443-453.
-
(1970)
J. Mol. Biol.
, vol.48
, pp. 443-453
-
-
Needleman, S.B.1
Wunsch, C.B.2
-
29
-
-
0027302043
-
Prediction of protein structure by evaluation of sequence-structure fitness. Aligning sequences to contact profiles derived from three-dimensional structures
-
Ouzounis C., Sander C., Scharf M., Schneider R. Prediction of protein structure by evaluation of sequence-structure fitness. Aligning sequences to contact profiles derived from three-dimensional structures. J. Mol. Biol. 232:1993;805-825.
-
(1993)
J. Mol. Biol.
, vol.232
, pp. 805-825
-
-
Ouzounis, C.1
Sander, C.2
Scharf, M.3
Schneider, R.4
-
30
-
-
0029063717
-
The complexity and accuracy of discrete state models of protein structure
-
Park B. H., Levitt M. The complexity and accuracy of discrete state models of protein structure. J. Mol. Biol. 249:1995;493-507.
-
(1995)
J. Mol. Biol.
, vol.249
, pp. 493-507
-
-
Park, B.H.1
Levitt, M.2
-
31
-
-
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. 258:1996;367-392.
-
(1996)
J. Mol. Biol.
, vol.258
, pp. 367-392
-
-
Park, B.1
Levitt, M.2
-
32
-
-
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. J. 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.J.1
-
33
-
-
0029000696
-
Knowledge-based potentials for proteins
-
Sippl M. J. Knowledge-based potentials for proteins. Curr. Opin. Struct. Biol. 5:1995;229-235.
-
(1995)
Curr. Opin. Struct. Biol.
, vol.5
, pp. 229-235
-
-
Sippl, M.J.1
-
34
-
-
0026704815
-
Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a data base of known protein conformations
-
Sippl M. J., 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: Struct. Funct. Genet. 13:1992;258-271.
-
(1992)
Proteins: Struct. Funct. Genet.
, vol.13
, pp. 258-271
-
-
Sippl, M.J.1
Weitckus, S.2
-
35
-
-
0029055313
-
LINUS: A hierarchic procedure to predict the fold of a protein
-
Srinivasan R., Rose G. D. LINUS: a hierarchic procedure to predict the fold of a protein. Proteins: Struct. Funct. Genet. 22:1995;81-99.
-
(1995)
Proteins: Struct. Funct. Genet.
, vol.22
, pp. 81-99
-
-
Srinivasan, R.1
Rose, G.D.2
-
36
-
-
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
-
37
-
-
0028841399
-
A simple protein folding algorithm using a binary code and secondary structure constraints
-
Sun S., Thomas P. D., Dill K. A. A simple protein folding algorithm using a binary code and secondary structure constraints. Protein Eng. 8:1995;769-778.
-
(1995)
Protein Eng.
, vol.8
, pp. 769-778
-
-
Sun, S.1
Thomas, P.D.2
Dill, K.A.3
-
39
-
-
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
-
40
-
-
0028290433
-
Prediction of the folding pathways and structure of the GCN4 leucine zipper
-
Vieth M., Kolinski A., Brooks C. L., III, Skolnick J. Prediction of the folding pathways and structure of the GCN4 leucine zipper. J. Mol. Biol. 237:1994;361-367.
-
(1994)
J. Mol. Biol.
, vol.237
, pp. 361-367
-
-
Vieth, M.1
Kolinski, A.2
Brooks C.L. III3
Skolnick, J.4
-
41
-
-
0029081216
-
Prediction of quaternary structure of coiled coils. Applications to mutants of the GCN4 leucine zipper
-
Vieth M., Kolinski A., Brooks C. L., III, Skolnick J. Prediction of quaternary structure of coiled coils. Applications to mutants of the GCN4 leucine zipper. J. Mol. Biol. 251:1995;448-467.
-
(1995)
J. Mol. Biol.
, vol.251
, pp. 448-467
-
-
Vieth, M.1
Kolinski, A.2
Brooks C.L. III3
Skolnick, J.4
-
42
-
-
0028347939
-
A simplified amino acid potential for use in structure prediction of proteins
-
Wallqvist A., Ullner M. A simplified amino acid potential for use in structure prediction 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
-
43
-
-
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
-
44
-
-
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
-
45
-
-
0027458885
-
Three-dimensional profiles from residue-pair preferences: Identification of sequences with β/α-barrel fold
-
Wilmanns M., Eisenberg D. Three-dimensional profiles from residue-pair preferences: identification of sequences with β/α-barrel fold. Proc. Natl Acad. Sci. USA, 90:1993;1379-1383.
-
(1993)
Proc. Natl Acad. Sci. USA
, vol.90
, pp. 1379-1383
-
-
Wilmanns, M.1
Eisenberg, D.2
-
46
-
-
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
-
47
-
-
0001018540
-
Analytical approximation to the accessible surface area of proteins
-
Wodak S. J., Janin J. Analytical approximation to the accessible surface area of proteins. Proc. Natl. Acad. Sci. USA. 77:1980;1736-1740.
-
(1980)
Proc. Natl. Acad. Sci. USA
, vol.77
, pp. 1736-1740
-
-
Wodak, S.J.1
Janin, J.2
-
49
-
-
0030048675
-
Folding proteins with a simple energy function and extensive conformational searching
-
Yue K., Dill K. A. Folding proteins with a simple energy function and extensive conformational searching. Protein Sci. 5:1996;254-261.
-
(1996)
Protein Sci.
, vol.5
, pp. 254-261
-
-
Yue, K.1
Dill, K.A.2
|