-
1
-
-
0031892528
-
Proteins fold recognition without Boltzman statistics or explicit physical basis
-
Huber T, Torda AE. Proteins fold recognition without Boltzman statistics or explicit physical basis. Protein Sci. 1998;7:142-149.
-
(1998)
Protein Sci.
, vol.7
, pp. 142-149
-
-
Huber, T.1
Torda, A.E.2
-
2
-
-
0037571112
-
Merck molecular force field. 1. Basis, form, scope, parameterization, and performance or MMFF94
-
Halgren TA. Merck molecular force field. 1. Basis, form, scope, parameterization, and performance or MMFF94. J Comput Chem 1996;17:490-519.
-
(1996)
J Comput Chem
, vol.17
, pp. 490-519
-
-
Halgren, T.A.1
-
3
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell AD, Bashford D, Bellott M, et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 1998;102:3586-3616.
-
(1998)
J Phys Chem B
, vol.102
, pp. 3586-3616
-
-
MacKerell, A.D.1
Bashford, D.2
Bellott, M.3
-
4
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell WD, Cieplak P, Bayly CI, et al. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 1995;117:5179-5197.
-
(1995)
J Am Chem Soc
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
-
6
-
-
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, 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
Lackner, P.2
Weitckus, S.3
-
7
-
-
0025341310
-
Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins
-
Sippl MJ. 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 1990;213: 859-883.
-
(1990)
J Mol Biol
, vol.213
, pp. 859-883
-
-
Sippl, M.J.1
-
8
-
-
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
-
9
-
-
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
-
10
-
-
0029945395
-
How optimization of potential functions affects protein folding
-
Hao MH, Scheraga HA. How optimization of potential functions affects protein folding. Proc Natl Acad Sci USA 1996;93:4984-4989.
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 4984-4989
-
-
Hao, M.H.1
Scheraga, H.A.2
-
11
-
-
0029895539
-
Self-consistently optimized statistical mechanical energy functions for sequence structure alignment
-
Koretke KK, Luthey-Schulten Z, Wolynes PG. Self-consistently optimized statistical mechanical energy functions for sequence structure alignment. Protein Sci 1996;5:1043-1059.
-
(1996)
Protein Sci
, vol.5
, pp. 1043-1059
-
-
Koretke, K.K.1
Luthey-Schulten, Z.2
Wolynes, P.G.3
-
12
-
-
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
-
13
-
-
0030975256
-
Protein structure prediction force fields - Parametrization with quasi-Newtonian dynamics
-
Ulrich P, Scott W, van Gunsteren WF, Torda AE. Protein structure prediction force fields - parametrization with quasi-Newtonian dynamics. Proteins 1997;27:367-384.
-
(1997)
Proteins
, vol.27
, pp. 367-384
-
-
Ulrich, P.1
Scott, W.2
Van Gunsteren, W.F.3
Torda, A.E.4
-
14
-
-
0032539910
-
Self-consistently optimized energy functions for protein structure prediction by molecular dynamics
-
Koretke KK, Luthey-Schulten Z, Wolynes PG. Self-consistently optimized energy functions for protein structure prediction by molecular dynamics. Proc Natl Acad Sci USA 1998;95:2932-2937.
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 2932-2937
-
-
Koretke, K.K.1
Luthey-Schulten, Z.2
Wolynes, P.G.3
-
15
-
-
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
-
16
-
-
0028015988
-
The protein threading problem with sequence amino acid interaction preferences is NP-complete
-
Lathrop RH. The protein threading problem with sequence amino acid interaction preferences is NP-complete. Protein Eng 1994;7: 1059-1068.
-
(1994)
Protein Eng
, vol.7
, pp. 1059-1068
-
-
Lathrop, R.H.1
-
17
-
-
0031865006
-
Touring protein fold space with Dali/FSSP
-
Holm L, Sander C. Touring protein fold space with Dali/FSSP. Nucleic Acids Res 1998;26:316-319.
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 316-319
-
-
Holm, L.1
Sander, C.2
-
18
-
-
0030765455
-
Dali/FSSP classification of three-dimensional protein folds
-
Holm L, Sander C. Dali/FSSP classification of three-dimensional protein folds. Nucleic Acids Res 1997;25:231-234.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 231-234
-
-
Holm, L.1
Sander, C.2
-
19
-
-
0029918694
-
The FSSP database - Fold classification based on structure-structure alignment of proteins
-
Holm L, Sander C. The FSSP database - fold classification based on structure-structure alignment of proteins. Nucleic Acids Res 1996;24:206-209.
-
(1996)
Nucleic Acids Res
, vol.24
, pp. 206-209
-
-
Holm, L.1
Sander, C.2
-
20
-
-
0027991446
-
The FSSP database of structurally aligned protein fold families
-
Holm L, Sander C. The FSSP database of structurally aligned protein fold families. Nucleic Acids Res 1994;22:3600-3609.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 3600-3609
-
-
Holm, L.1
Sander, C.2
-
21
-
-
0029982530
-
The structural alignment between two proteins: Is there a unique answer?
-
Godzik A. The structural alignment between two proteins: is there a unique answer? Protein Sci 1996;5:1325-1338.
-
(1996)
Protein Sci
, vol.5
, pp. 1325-1338
-
-
Godzik, A.1
-
22
-
-
0030334647
-
Optimum superimposition of protein structures: Ambiguities and implications
-
Feng ZK, Sippl MJ. Optimum superimposition of protein structures: ambiguities and implications. Fold Des 1996;1:123-132.
-
(1996)
Fold Des
, vol.1
, pp. 123-132
-
-
Feng, Z.K.1
Sippl, M.J.2
-
23
-
-
0002638513
-
Protein data bank
-
Allen FH, Bergerhoff G, Sievers R. Bonn, Cambridge, Chester: Data Commission of the International Union of Crystallography
-
Abola EE, Bernstein FC, Bryant SH, Koetzle TF, Weng J. Protein data bank. In: Allen FH, Bergerhoff G, Sievers R. Crystallographic databases-information content, software systems, scientific applications. Bonn, Cambridge, Chester: Data Commission of the International Union of Crystallography; 1987. p 107-132.
-
(1987)
Crystallographic Databases-information Content, Software Systems, Scientific Applications
, pp. 107-132
-
-
Abola, E.E.1
Bernstein, F.C.2
Bryant, S.H.3
Koetzle, T.F.4
Weng, J.5
-
24
-
-
0030847766
-
Protein data bank archives of three-dimensional macromolecular structures
-
Abola EE, Sussman JL, Prilusky J, Manning NO. Protein data bank archives of three-dimensional macromolecular structures. Methods Enzymol 1997;277:556-571.
-
(1997)
Methods Enzymol
, vol.277
, pp. 556-571
-
-
Abola, E.E.1
Sussman, J.L.2
Prilusky, J.3
Manning, N.O.4
-
25
-
-
0027092678
-
Selection of a representative set of structures from the Brookhaven protein data bank
-
Hobohm U, Scharf M, Schneider R, Sander C. Selection of a representative set of structures from the Brookhaven protein data bank. Protein Sci 1992;1:409-417.
-
(1992)
Protein Sci
, vol.1
, pp. 409-417
-
-
Hobohm, U.1
Scharf, M.2
Schneider, R.3
Sander, C.4
-
26
-
-
0028205447
-
Enlarged representative set of protein structures
-
Hobohm U, Sander C. Enlarged representative set of protein structures. Protein Sci 1994;3:522-524.
-
(1994)
Protein Sci
, vol.3
, pp. 522-524
-
-
Hobohm, U.1
Sander, C.2
-
27
-
-
0031577260
-
Protein fold recognition by prediction-based threading
-
Rost B, Schneider R, Sander C. Protein fold recognition by prediction-based threading. J Mol Biol 1997;270:471-480.
-
(1997)
J Mol Biol
, vol.270
, pp. 471-480
-
-
Rost, B.1
Schneider, R.2
Sander, C.3
-
29
-
-
0000817556
-
Protein sequence threading, the alignment problem and a two step strategy
-
in press
-
Huber T, Torda AE. Protein sequence threading, the alignment problem and a two step strategy. J Comput Chem 1999; in press.
-
(1999)
J Comput Chem
-
-
Huber, T.1
Torda, A.E.2
-
30
-
-
0014757386
-
A general method applicable to the search for similarities in the amino acid sequence of two proteins
-
Needleman SB, Wunsch CD. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 1970;48:443-453.
-
(1970)
J. Mol. Biol.
, vol.48
, pp. 443-453
-
-
Needleman, S.B.1
Wunsch, C.D.2
-
31
-
-
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. 1992;227:227-238.
-
(1992)
J. Mol. Biol.
, vol.227
, pp. 227-238
-
-
Godzik, A.1
Kolinski, A.2
Skolnick, J.3
-
32
-
-
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
-
33
-
-
0028886967
-
Inverse protein folding by the residue pair preference profile method: Estimating the correctness of alignments of structurally compatible sequences
-
Wilmanns M, Eisenberg D. Inverse protein folding by the residue pair preference profile method: estimating the correctness of alignments of structurally compatible sequences. Protein Eng 1995;8:627-639.
-
(1995)
Protein Eng
, vol.8
, pp. 627-639
-
-
Wilmanns, M.1
Eisenberg, D.2
-
34
-
-
44949272730
-
A time-efficient, linear-space local similarity algorithm
-
Huang X, Miller W. A time-efficient, linear-space local similarity algorithm. Adv Appl Math 1991;12:337-357.
-
(1991)
Adv Appl Math
, vol.12
, pp. 337-357
-
-
Huang, X.1
Miller, W.2
-
36
-
-
0028318094
-
Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches
-
Kocher JPA, 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
-
37
-
-
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
|