-
1
-
-
0029097099
-
Global fold determination from a small number of distance restraints
-
Aszodi A., Gradwell M. J., Taylor W. R. Global fold determination from a small number of distance restraints. J. Mol. Biol. 251:1995;308-326.
-
(1995)
J. Mol. Biol.
, vol.251
, pp. 308-326
-
-
Aszodi, A.1
Gradwell, M.J.2
Taylor, W.R.3
-
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
-
-
0031747982
-
A combinatorial distance-constraint approach to predicting protein tertiary models from known secondary structure
-
Chelvanayagam G., Knecht L., Jenny T., Benner S. A., Gonnet G. H. A combinatorial distance-constraint approach to predicting protein tertiary models from known secondary structure. Fold. Design. 3:1998;149-160.
-
(1998)
Fold. Design
, vol.3
, pp. 149-160
-
-
Chelvanayagam, G.1
Knecht, L.2
Jenny, T.3
Benner, S.A.4
Gonnet, G.H.5
-
4
-
-
0033021805
-
Using imperfect secondary structure predictions to improve molecular structure computations
-
Chen C. C., Singh J. P., Altman R. B. Using imperfect secondary structure predictions to improve molecular structure computations. Bioinformatics. 15:1999;53-65.
-
(1999)
Bioinformatics
, vol.15
, pp. 53-65
-
-
Chen, C.C.1
Singh, J.P.2
Altman, R.B.3
-
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 alpha-carbon chains into compact forms by Monte Carlo methods
-
Covell D. G. Folding protein alpha-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
-
-
0009636533
-
Protein folding simulation with genetic algorithm and supersecondary structure constraints
-
Cui Y., Chen R. S., Wong W. H. Protein folding simulation with genetic algorithm and supersecondary structure constraints. Proteins: Struct. Funct. Genet. 31:1998;247-257.
-
(1998)
Proteins: Struct. Funct. Genet.
, vol.31
, pp. 247-257
-
-
Cui, Y.1
Chen, R.S.2
Wong, W.H.3
-
8
-
-
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
-
-
0025932859
-
An evaluation of computational strategies for use in the determination of protein structure from distance constraints obtained by nuclear magnetic resonance
-
Havel T. F. An evaluation of computational strategies for use in the determination of protein structure from distance constraints obtained by nuclear magnetic resonance. Prog. Biophys. Mol. Biol. 56:1991;43-78.
-
(1991)
Prog. Biophys. Mol. Biol.
, vol.56
, pp. 43-78
-
-
Havel, T.F.1
-
11
-
-
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
-
12
-
-
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
-
13
-
-
0030573021
-
The NMR solution structure of intestinal fatty acid-binding protein complexed with palmitate: Application of a novel distance geometry algorithm
-
Hodsdon M. E., Ponder J. W., Cistola D. P. The NMR solution structure of intestinal fatty acid-binding protein complexed with palmitate: application of a novel distance geometry algorithm. J. Mol. Biol. 264:1996;585-602.
-
(1996)
J. Mol. Biol.
, vol.264
, pp. 585-602
-
-
Hodsdon, M.E.1
Ponder, J.W.2
Cistola, D.P.3
-
14
-
-
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
-
15
-
-
0031687654
-
Distance geometry generates native-like folds for small helical proteins using the consensus distances of predicted protein structures
-
Huang E. S., Samudrala R., Ponder J. W. Distance geometry generates native-like folds for small helical proteins using the consensus distances of predicted protein structures. Protein Sci. 7:1998;1998-2003.
-
(1998)
Protein Sci.
, vol.7
, pp. 1998-2003
-
-
Huang, E.S.1
Samudrala, R.2
Ponder, J.W.3
-
16
-
-
0003742069
-
-
Department of Biochemistry and Molecular BiologyUniversity College London
-
Hubbard S. J., Thornton J. M. 'NACCESS' Computer Program. 1993;Department of Biochemistry and Molecular BiologyUniversity College London.
-
(1993)
'NACCESS' Computer Program
-
-
Hubbard, S.J.1
Thornton, J.M.2
-
18
-
-
0031298075
-
Successful ab initio prediction of the tertiary structure of NK-lysin using multiple sequences and recognized supersecondary structural motifs
-
Jones D. T. Successful ab initio prediction of the tertiary structure of NK-lysin using multiple sequences and recognized supersecondary structural motifs. Proteins: Struct. Funct. Genet. Suppl 1:1997;185-191.
-
(1997)
Proteins: Struct. Funct. Genet.
, vol.1
, pp. 185-191
-
-
Jones, D.T.1
-
19
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch W., Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 22:1983;2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
20
-
-
0026754015
-
Accurate modeling of protein conformation by automatic segment matching
-
Levitt M. Accurate modeling of protein conformation by automatic segment matching. J. Mol. Biol. 226:1992;507-533.
-
(1992)
J. Mol. Biol.
, vol.226
, pp. 507-533
-
-
Levitt, M.1
-
21
-
-
0029633167
-
Potential-energy function and parameters for simulations of the molecular-dynamics of proteins and nucleic-acids in solution
-
Levitt M., Hirshberg M., Sharon R., Daggett V. Potential-energy function and parameters for simulations of the molecular-dynamics of proteins and nucleic-acids in solution. Comput. Phys. Commun. 91:1995;215-231.
-
(1995)
Comput. Phys. Commun.
, vol.91
, pp. 215-231
-
-
Levitt, M.1
Hirshberg, M.2
Sharon, R.3
Daggett, V.4
-
22
-
-
0029846867
-
Relationship between protein structure and geometrical constraints
-
Lund O., Hansen J., Brunak S., Bohr J. Relationship between protein structure and geometrical constraints. Protein Sci. 5:1996;2217-2225.
-
(1996)
Protein Sci.
, vol.5
, pp. 2217-2225
-
-
Lund, O.1
Hansen, J.2
Brunak, S.3
Bohr, J.4
-
23
-
-
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 P. 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, P.S.4
Friesner, R.A.5
-
24
-
-
0028955505
-
Predicting the helix packing of globular proteins by self-correcting distance geometry
-
Mumenthaler C., Braun W. Predicting the helix packing of globular proteins by self-correcting distance geometry. Protein Sci. 4:1995;863-871.
-
(1995)
Protein Sci.
, vol.4
, pp. 863-871
-
-
Mumenthaler, C.1
Braun, W.2
-
25
-
-
0032571390
-
Fold assembly of small proteins using monte carlo simulations driven by restraints derived from multiple sequence alignments
-
Ortiz A. R., Kolinski A., Skolnick J. Fold assembly of small proteins using monte carlo simulations driven by restraints derived from multiple sequence alignments. J. Mol. Biol. 277:1998;419-448.
-
(1998)
J. Mol. Biol.
, vol.277
, pp. 419-448
-
-
Ortiz, A.R.1
Kolinski, A.2
Skolnick, J.3
-
26
-
-
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
-
27
-
-
0029987862
-
Energy functions that discriminate X-ray and near native folds from well-constructed docoys
-
Park B. H., Levitt M. Energy functions that discriminate X-ray and near native folds from well-constructed docoys. J. Mol. Biol. 258:1996;367-392.
-
(1996)
J. Mol. Biol.
, vol.258
, pp. 367-392
-
-
Park, B.H.1
Levitt, M.2
-
28
-
-
0031557390
-
Factors affecting the ability of energy functions to discriminate correct from incorrect folds
-
Park B. H., Huang E. S., Levitt M. Factors affecting the ability of energy functions to discriminate correct from incorrect folds. J. Mol. Biol. 266:1995;831-846.
-
(1995)
J. Mol. Biol.
, vol.266
, pp. 831-846
-
-
Park, B.H.1
Huang, E.S.2
Levitt, M.3
-
29
-
-
0031556019
-
Protein folding simulations with genetic algorithms and a detailed molecular description
-
Pedersen J. T., Moult J. Protein folding simulations with genetic algorithms and a detailed molecular description. J. Mol. Biol. 269:1997;240-259.
-
(1997)
J. Mol. Biol.
, vol.269
, pp. 240-259
-
-
Pedersen, J.T.1
Moult, J.2
-
30
-
-
0000939821
-
What is the probability of a chance prediction of a protein structure with an rmsd of 6 A?
-
Reva B. A., Finkelstein A. V., Skolnick J. What is the probability of a chance prediction of a protein structure with an rmsd of 6 A? Fold. Design. 3:1998;141-147.
-
(1998)
Fold. Design
, vol.3
, pp. 141-147
-
-
Reva, B.A.1
Finkelstein, A.V.2
Skolnick, J.3
-
31
-
-
0028158628
-
PHD - an automatic mail server for protein secondary structure prediction
-
Rost B., Sander C., Schneider R. PHD - an automatic mail server for protein secondary structure prediction. Comput. Appl. Biosci. 10:1994;53-60.
-
(1994)
Comput. Appl. Biosci.
, vol.10
, pp. 53-60
-
-
Rost, B.1
Sander, C.2
Schneider, R.3
-
32
-
-
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. 275:1998;895-916.
-
(1998)
J. Mol. Biol.
, vol.275
, pp. 895-916
-
-
Samudrala, R.1
Moult, J.2
-
33
-
-
0032611514
-
A combined approach for ab initio construction of low resolution protein tertiary structures from sequence
-
Samudrala R., Xia Y., Levitt M., Huang E. S. A combined approach for ab initio construction of low resolution protein tertiary structures from sequence. Proc. Pac. Symp. Biocomput. 1999;505-516.
-
(1999)
Proc. Pac. Symp. Biocomput.
, pp. 505-516
-
-
Samudrala, R.1
Xia, Y.2
Levitt, M.3
Huang, E.S.4
-
34
-
-
0026030641
-
Database of homology-derived protein structures and the structural meaning of sequence alignment
-
Sander C., Schneider R. Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins: Struct. Funct. Genet. 9:1991;56-68.
-
(1991)
Proteins: Struct. Funct. Genet.
, vol.9
, pp. 56-68
-
-
Sander, C.1
Schneider, R.2
-
35
-
-
0031585984
-
Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
-
Simons K. T., Kooperberg C., Huang E., Baker D. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J. Mol. Biol. 268:1997;209-225.
-
(1997)
J. Mol. Biol.
, vol.268
, pp. 209-225
-
-
Simons, K.T.1
Kooperberg, C.2
Huang, E.3
Baker, D.4
-
36
-
-
0027168790
-
Global folding of proteins using a limited number of distance constraints
-
Smith-Brown M. J., Kominos D., Levy R. M. Global folding of proteins using a limited number of distance constraints. Protein Eng. 6:1993;605-614.
-
(1993)
Protein Eng.
, vol.6
, pp. 605-614
-
-
Smith-Brown, M.J.1
Kominos, D.2
Levy, R.M.3
-
37
-
-
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
-
38
-
-
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
-
-
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
-
41
-
-
0033003903
-
Sequence specificity, statistical potentials, and three-dimensional structure prediction with self-correcting distance geometry calculations of β-sheet formation in proteins
-
Zhu H. Y., Braun W. Sequence specificity, statistical potentials, and three-dimensional structure prediction with self-correcting distance geometry calculations of β-sheet formation in proteins. Protein Sci. 8:1999;326-342.
-
(1999)
Protein Sci.
, vol.8
, pp. 326-342
-
-
Zhu, H.Y.1
Braun, W.2
|