-
1
-
-
36449005845
-
A deterministic global optimization approach for molecular structure determination
-
Costas MD, Floudas CA. A deterministic global optimization approach for molecular structure determination. J Chem Phys 1994;100:1247-1261.
-
(1994)
J Chem Phys
, vol.100
, pp. 1247-1261
-
-
Costas, M.D.1
Floudas, C.A.2
-
2
-
-
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 1992;18:338-352.
-
(1992)
Proteins
, vol.18
, pp. 338-352
-
-
Kolinski, A.1
Skolnick, J.2
-
3
-
-
0028283339
-
An algorithm to generate low-resolution protein tertiary structures from a knowledge of secondary structure
-
Monge A, Friesner RA, Honig B. An algorithm to generate low-resolution protein tertiary structures from a knowledge of secondary structure. Proc Natl Acad Sci USA 1994;91:5027-5029.
-
(1994)
Proc Natl Acad Sci USA
, vol.91
, pp. 5027-5029
-
-
Monge, A.1
Friesner, R.A.2
Honig, B.3
-
4
-
-
0028897718
-
Computer modeling of protein folding: Conformational and energetic analysis of reduced and detailed protein models
-
Monge A, Lathrop E, Gunn JR, Shenkin PS, Friesner RA. Computer modeling of protein folding: conformational and energetic analysis of reduced and detailed protein models. J Mol Biol 1995;247:995-1012.
-
(1995)
J Mol Biol
, vol.247
, pp. 995-1012
-
-
Monge, A.1
Lathrop, E.2
Gunn, J.R.3
Shenkin, P.S.4
Friesner, R.A.5
-
5
-
-
0000335209
-
Hierarchical algorithm for computer modeling of protein tertiary structure: Folding of myoglobin to 6.2Å resolution
-
Gunn JR, Monge A, Friesner RA, Marshall CH. Hierarchical algorithm for computer modeling of protein tertiary structure: folding of myoglobin to 6.2Å resolution. J Phys Chem 1994;98:702-711.
-
(1994)
J Phys Chem
, vol.98
, pp. 702-711
-
-
Gunn, J.R.1
Monge, A.2
Friesner, R.A.3
Marshall, Ch.4
-
6
-
-
0004498733
-
Parallel implementation of a protein structure refinement algorithm
-
Gunn JR, Friesner RA. Parallel implementation of a protein structure refinement algorithm. J Comp Chem 1996;17:1217-1228.
-
(1996)
J Comp Chem
, vol.17
, pp. 1217-1228
-
-
Gunn, J.R.1
Friesner, R.A.2
-
7
-
-
0031720235
-
Tertiary structure prediction of mixed α/β proteins via energy minimization
-
Standley DM, Gunn JR, Friesner RA, McDermott AE. Tertiary structure prediction of mixed α/β proteins via energy minimization. Proteins 1998;33:240-252.
-
(1998)
Proteins
, vol.33
, pp. 240-252
-
-
Standley, D.M.1
Gunn, J.R.2
Friesner, R.A.3
McDermott, A.E.4
-
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 1996;256:645-660.
-
(1996)
J Mol Biol
, vol.256
, pp. 645-660
-
-
Dandekar, T.1
Argos, P.2
-
9
-
-
0026539511
-
Structure-derived hydrophobic potential
-
Casari G, Sippl MJ. Structure-derived hydrophobic potential. J Mol Biol 1992;224:725-732.
-
(1992)
J Mol Biol
, vol.224
, pp. 725-732
-
-
Casari, G.1
Sippl, M.J.2
-
10
-
-
0017411710
-
The protein data bank: A computer-based archival file for macromolecular structures
-
Berstein 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
-
-
Berstein, F.C.1
Koetzle, T.F.2
Williams, G.J.B.3
-
11
-
-
0002638513
-
Protein data bank
-
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: 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
-
12
-
-
0001327501
-
αBB: A global optimization method for general constrained nonconvex problems
-
CDM
-
Androulakis IP, CDM, Floudas CA. αBB: A global optimization method for general constrained nonconvex problems. J Glob Optim 1995;7:337-363.
-
(1995)
J Glob Optim
, vol.7
, pp. 337-363
-
-
Androulakis, I.P.1
Floudas, C.A.2
-
13
-
-
0028049306
-
Lattice model simulations of polypeptide chain folding
-
Covell DG. Lattice model simulations of polypeptide chain folding. J Mol Biol 1994;235:1032-1043.
-
(1994)
J Mol Biol
, vol.235
, pp. 1032-1043
-
-
Covell, D.G.1
-
14
-
-
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
-
15
-
-
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
-
16
-
-
33845377127
-
Estimation of effective inter-residue contact energies from protein crystal structures
-
Miyazawa S, Jernigan RL. Estimation of effective inter-residue contact energies from protein crystal structures. Macromolecules 1985;18:534-552.
-
(1985)
Macromolecules
, vol.18
, pp. 534-552
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
17
-
-
0025319917
-
Conformations of folded proteins in restricted spaces
-
Covell DG, Jernigan RL. Conformations of folded proteins in restricted spaces. Biochemistry 1990;29:3287-3294.
-
(1990)
Biochemistry
, vol.29
, pp. 3287-3294
-
-
Covell, D.G.1
Jernigan, R.L.2
-
18
-
-
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
-
19
-
-
84986437005
-
Macro model - An integrated software system for modeling organic and bioorganic molecules using molecular mechanics
-
Mohamadi R, Richards NGJ, Guida WC, et al. Macro Model - An integrated software system for modeling organic and bioorganic molecules using molecular mechanics. J Comput Chem 1990;11: 440-467.
-
(1990)
J Comput Chem
, vol.11
, pp. 440-467
-
-
Mohamadi, R.1
Richards, N.G.J.2
Guida, W.C.3
-
20
-
-
0021757436
-
A new force field for molecular mechanical simulation of nucleic acids and proteins
-
Weiner SJ, Kollman PA, Case DA, et al. A new force field for molecular mechanical simulation of nucleic acids and proteins. J Am Chem Soc 1984;106:765-784.
-
(1984)
J Am Chem Soc
, vol.106
, pp. 765-784
-
-
Weiner, S.J.1
Kollman, P.A.2
Case, D.A.3
-
21
-
-
84988053694
-
An all atom force field for simulations of proteins and nucleic acids
-
Weiner S, Kollman PA, Nguyen DT, Case DA. An all atom force field for simulations of proteins and nucleic acids. J Comput Chem 1986;7:230-252.
-
(1986)
J Comput Chem
, vol.7
, pp. 230-252
-
-
Weiner, S.1
Kollman, P.A.2
Nguyen, D.T.3
Case, D.A.4
-
23
-
-
0344095828
-
-
London: Butterworths Scientific Publications
-
Booth AD. Numerical methods. 2nd ed. London: Butterworths Scientific Publications; 1957.
-
(1957)
Numerical Methods. 2nd Ed.
-
-
Booth, A.D.1
-
24
-
-
0026761547
-
Folding protein α-carbon chains into compact forms by Monte Carlo methods
-
Covell DG. Folding protein α-carbon chains into compact forms by Monte Carlo methods. Proteins 1992;14:409-420.
-
(1992)
Proteins
, vol.14
, pp. 409-420
-
-
Covell, D.G.1
-
25
-
-
0001194908
-
Discretized model of proteins. I. Monte carlo study of cooperativity in homopolypeptides
-
Kolinski A, Skolnick J. Discretized model of proteins. I. Monte Carlo study of cooperativity in homopolypeptides. J Chem Phys 1992;97:9412-9426.
-
(1992)
J Chem Phys
, vol.97
, pp. 9412-9426
-
-
Kolinski, A.1
Skolnick, J.2
-
26
-
-
0029984690
-
Genetic algorithms for protein structure prediction
-
Pedersen JT, Moult J. Genetic algorithms for protein structure prediction. Curr Opin Struc Biol 1996;6:227-231.
-
(1996)
Curr Opin Struc Biol
, vol.6
, pp. 227-231
-
-
Pedersen, J.T.1
Moult, J.2
-
27
-
-
0031556019
-
Protein folding simulations with genetic algorithms and a detailed molecular description
-
Pedersen JT. Moult J. Protein folding simulations with genetic algorithms and a detailed molecular description. J Mol Biol 1997;269:240-259.
-
(1997)
J Mol Biol
, vol.269
, pp. 240-259
-
-
Pedersen Jt Moult, J.1
-
28
-
-
0029132872
-
A genetic algorithm that seeks native states of peptides and proteins
-
Sun S. A genetic algorithm that seeks native states of peptides and proteins. Biophys J 1995;69:340-355.
-
(1995)
Biophys J
, vol.69
, pp. 340-355
-
-
Sun, S.1
-
29
-
-
0021095856
-
Protein folding by restrained energy minimization
-
Levitt M. Protein folding by restrained energy minimization J Mol Biol 1983;170:723-764.
-
(1983)
J Mol Biol
, vol.170
, pp. 723-764
-
-
Levitt, M.1
-
33
-
-
0032571390
-
Fold assembly of small proteins using Monte Carlo simulations driven by restraints derived from multiple sequence alignments
-
Ortiz AR, Kolinski A, Skolnick J. Fold assembly of small proteins using Monte Carlo simulations driven by restraints derived from multiple sequence alignments. J Mol Biol 1998;277:419-448.
-
(1998)
J Mol Biol
, vol.277
, pp. 419-448
-
-
Ortiz, A.R.1
Kolinski, A.2
Skolnick, J.3
-
34
-
-
0033613919
-
A branch and bound algorithm for protein structure refinement from sparse NMR data sets
-
Standey DM, Eyrich VA, Felts AK, Friesner RA, McDermott AE. A branch and bound algorithm for protein structure refinement from sparse NMR data sets. J Mol Biol 1999;285:1689-1708.
-
(1999)
J Mol Biol
, vol.285
, pp. 1689-1708
-
-
Standey, D.M.1
Eyrich, V.A.2
Felts, A.K.3
Friesner, R.A.4
McDermott, A.E.5
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