-
1
-
-
0028300741
-
Combining evolutionary information and neural networks to predict protein secondary structure
-
Rost B, Sander C. Combining evolutionary information and neural networks to predict protein secondary structure. Proteins 1994;19:55-72.
-
(1994)
Proteins
, vol.19
, pp. 55-72
-
-
Rost, B.1
Sander, C.2
-
2
-
-
0033578684
-
Protein secondary structure prediction based on position-specific scoring matrices
-
Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999;292:195-202.
-
(1999)
J Mol Biol
, vol.292
, pp. 195-202
-
-
Jones, D.T.1
-
3
-
-
0032555696
-
Prediction of local structure in proteins using a library of sequence-structure motifs
-
Bystroff C, Baker D. Prediction of local structure in proteins using a library of sequence-structure motifs. J Mol Biol 1998;281:565-577.
-
(1998)
J Mol Biol
, vol.281
, pp. 565-577
-
-
Bystroff, C.1
Baker, D.2
-
4
-
-
0034604368
-
HMMSTR: A hidden Markov model for local sequence-structure correlations in proteins
-
Bystroff C, Thorsson V, Baker D. HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins. J Mol Biol 2002;301:173-190.
-
(2002)
J Mol Biol
, vol.301
, pp. 173-190
-
-
Bystroff, C.1
Thorsson, V.2
Baker, D.3
-
5
-
-
0027174134
-
Prediction of protein secondary structure by the hidden Markov model
-
Asai K, Hayamizu S, Handa K. Prediction of protein secondary structure by the hidden Markov model. Comput Appl Biosci 1993;9:141-146.
-
(1993)
Comput Appl Biosci
, vol.9
, pp. 141-146
-
-
Asai, K.1
Hayamizu, S.2
Handa, K.3
-
6
-
-
0031585987
-
Protein secondary structure prediction using local alignments
-
Salamov AA, Solovyev VV. Protein secondary structure prediction using local alignments. J Mol Biol 1997;268:31-36.
-
(1997)
J Mol Biol
, vol.268
, pp. 31-36
-
-
Salamov, A.A.1
Solovyev, V.V.2
-
7
-
-
0020446736
-
Coiled-coils in alpha-helix-containing proteins: Analysis of the residue types within the heptad repeat and the use of these data in the prediction of coiled-coils in other proteins
-
Parry DA. Coiled-coils in alpha-helix-containing proteins: analysis of the residue types within the heptad repeat and the use of these data in the prediction of coiled-coils in other proteins. Biosci Rep 1982;2:1017-1024.
-
(1982)
Biosci Rep
, vol.2
, pp. 1017-1024
-
-
Parry, D.A.1
-
8
-
-
0027165688
-
Peptide models of protein folding initiation sites. I. Secondary structure formation by peptides corresponding to the G- and H-helices of myoglobin
-
Waltho JP, Feher VA, Merutka G, Dyson HJ, Wright PE. Peptide models of protein folding initiation sites. I. Secondary structure formation by peptides corresponding to the G- and H-helices of myoglobin. Biochemistry 1993;32:6337-6347.
-
(1993)
Biochemistry
, vol.32
, pp. 6337-6347
-
-
Waltho, J.P.1
Feher, V.A.2
Merutka, G.3
Dyson, H.J.4
Wright, P.E.5
-
9
-
-
0343059020
-
Conformational analysis of peptides corresponding to beta-hairpins and a beta-sheet that represent the entire sequence of the alpha-spectrin SH3 domain
-
Viguera AR, Jimenez MA, Rico M, Serrano L. Conformational analysis of peptides corresponding to beta-hairpins and a beta-sheet that represent the entire sequence of the alpha-spectrin SH3 domain. J Mol Biol 1996;255:507-521.
-
(1996)
J Mol Biol
, vol.255
, pp. 507-521
-
-
Viguera, A.R.1
Jimenez, M.A.2
Rico, M.3
Serrano, L.4
-
10
-
-
0027984190
-
Synthetic peptides probe folding initiation sites in platelet factor 4: Stable chain reversal found within the hydrophobic sequence LIATLKNGRKISL
-
Ilyina E, Milius R, Mayo KH. Synthetic peptides probe folding initiation sites in platelet factor 4: stable chain reversal found within the hydrophobic sequence LIATLKNGRKISL. Biochemistry 1994;33:13436-13444.
-
(1994)
Biochemistry
, vol.33
, pp. 13436-13444
-
-
Ilyina, E.1
Milius, R.2
Mayo, K.H.3
-
11
-
-
0029053552
-
Folding of a nascent polypeptide chain in vitro: Cooperative of structure in a protein module
-
De Prat Gay G, Ruiz-Sanz J, Neira JL, Itzhaki LS, Fersht AR. Folding of a nascent polypeptide chain in vitro: cooperative of structure in a protein module. Proc Natl Acad Sci USA 1995;92:3683-3686.
-
(1995)
Proc Natl Acad Sci USA
, vol.92
, pp. 3683-3686
-
-
De Prat Gay, G.1
Ruiz-Sanz, J.2
Neira, J.L.3
Itzhaki, L.S.4
Fersht, A.R.5
-
12
-
-
0032538302
-
Prediction and structural characterization of an independently folding substructure in the src SH3 domain
-
Yi Q, Bystroff C, Rajagopal P, Klevit RE, Baker D. Prediction and structural characterization of an independently folding substructure in the src SH3 domain. J Mol Biol 1998;283:293-300.
-
(1998)
J Mol Biol
, vol.283
, pp. 293-300
-
-
Yi, Q.1
Bystroff, C.2
Rajagopal, P.3
Klevit, R.E.4
Baker, D.5
-
13
-
-
0031301753
-
Blind predictions of local protein structure in CASP2 targets using the I-sites library
-
Bystroff C, Baker D. Blind predictions of local protein structure in CASP2 targets using the I-sites library. Proteins 1997;(Suppl 1):167-171.
-
(1997)
Proteins
, Issue.SUPPL. 1
, pp. 167-171
-
-
Bystroff, C.1
Baker, D.2
-
14
-
-
0029633186
-
AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules
-
Pearlman DA, Case DA, Caldwell JW, et al. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comput Phys Commun 1995;91:1-41.
-
(1995)
Comput Phys Commun
, vol.91
, pp. 1-41
-
-
Pearlman, D.A.1
Case, D.A.2
Caldwell, J.W.3
-
15
-
-
84986518863
-
AMBER: Assisted model building with energy refinement - A general program for modeling molecules and their interactions
-
Weiner PK, Kollman PA. AMBER: assisted model building with energy refinement - a general program for modeling molecules and their interactions. J Comput Chem 1981;2:287-303.
-
(1981)
J Comput Chem
, vol.2
, pp. 287-303
-
-
Weiner, P.K.1
Kollman, P.A.2
-
16
-
-
0035135910
-
Folding study of an Aib-rich peptide in DMSO by molecular dynamics simulations
-
Burgi R, Daura X, Mark A, et al. Folding study of an Aib-rich peptide in DMSO by molecular dynamics simulations. J Pept Res 2001;57:107-118.
-
(2001)
J Pept Res
, vol.57
, pp. 107-118
-
-
Burgi, R.1
Daura, X.2
Mark, A.3
-
17
-
-
0041140017
-
Simulations of peptide conformational dynamics and thermodynamics
-
Brooks C, Case D. Simulations of peptide conformational dynamics and thermodynamics. Chem Rev 1993;93:2487-2502.
-
(1993)
Chem Rev
, vol.93
, pp. 2487-2502
-
-
Brooks, C.1
Case, D.2
-
18
-
-
0034033187
-
Long timescale simulations
-
Daggett V. Long timescale simulations. Curr Opin Struct Biol 2000;10:160-164.
-
(2000)
Curr Opin Struct Biol
, vol.10
, pp. 160-164
-
-
Daggett, V.1
-
19
-
-
0035179018
-
Helix nucleation kinetics from molecular simulations in explicit solvent
-
Hummer G, Garcia AE, Garde S. Helix nucleation kinetics from molecular simulations in explicit solvent. Proteins 2001;42:77-84.
-
(2001)
Proteins
, vol.42
, pp. 77-84
-
-
Hummer, G.1
Garcia, A.E.2
Garde, S.3
-
20
-
-
0034718553
-
Folding simulations of a three-stranded antiparallel beta-sheet peptide
-
Ferrara P, Caflisch A. Folding simulations of a three-stranded antiparallel beta-sheet peptide. Proc Natl Acad Sci USA 2000;97:10780-10785.
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 10780-10785
-
-
Ferrara, P.1
Caflisch, A.2
-
21
-
-
0030068825
-
Interactions contributing to the formation of a beta-hairpin-like structure in a small peptide
-
Sieber V, Moe GR. Interactions contributing to the formation of a beta-hairpin-like structure in a small peptide. Biochemistry 1996;35:181-188.
-
(1996)
Biochemistry
, vol.35
, pp. 181-188
-
-
Sieber, V.1
Moe, G.R.2
-
22
-
-
0030334822
-
Conformational investigation of designed short linear peptides able to fold into beta-hairpin structures in aqueous solution
-
de Alba E, Jimenez MA, Rico M, Nieto JL. Conformational investigation of designed short linear peptides able to fold into beta-hairpin structures in aqueous solution. Fold Des 1996;1:133-144.
-
(1996)
Fold Des
, vol.1
, pp. 133-144
-
-
De Alba, E.1
Jimenez, M.A.2
Rico, M.3
Nieto, J.L.4
-
23
-
-
0028500779
-
A short linear peptide that folds into a native stable beta-hairpin in aqueous solution
-
Blanco FJ, Rivas G, Serrano L. A short linear peptide that folds into a native stable beta-hairpin in aqueous solution. Nat Struct Biol 1994;1:584-590.
-
(1994)
Nat Struct Biol
, vol.1
, pp. 584-590
-
-
Blanco, F.J.1
Rivas, G.2
Serrano, L.3
-
24
-
-
0028820601
-
Analysis of i,i+5 and i,i+8 hydrophobic interactions in a helical model peptide bearing the hydrophobic staple motif
-
Munoz V, Serrano L. Analysis of i,i+5 and i,i+8 hydrophobic interactions in a helical model peptide bearing the hydrophobic staple motif. Biochemistry 1995;34:15301-15306.
-
(1995)
Biochemistry
, vol.34
, pp. 15301-15306
-
-
Munoz, V.1
Serrano, L.2
-
25
-
-
0030002295
-
Native-like beta-hairpin structure in an isolated fragment from ferredoxin: NMR and CD studies of solvent effects on the N-terminal 20 residues
-
Searle MS, Zerella R, Williams DH, Packman LC. Native-like beta-hairpin structure in an isolated fragment from ferredoxin: NMR and CD studies of solvent effects on the N-terminal 20 residues. Protein Eng 1996;9:559-565.
-
(1996)
Protein Eng
, vol.9
, pp. 559-565
-
-
Searle, M.S.1
Zerella, R.2
Williams, D.H.3
Packman, L.C.4
-
26
-
-
0035479690
-
Molecular dynamics simulations of a highly charged peptide from an SH3 domain: Possible sequence-function relationship
-
Krueger BP, Kollman PA. Molecular dynamics simulations of a highly charged peptide from an SH3 domain: possible sequence-function relationship. Proteins 2001;45:4-15.
-
(2001)
Proteins
, vol.45
, pp. 4-15
-
-
Krueger, B.P.1
Kollman, P.A.2
-
27
-
-
0030914617
-
Comparison of database potentials and molecular mechanics force fields
-
Moult J. Comparison of database potentials and molecular mechanics force fields. Curr Opin Struct Biol 1997;7:194-199.
-
(1997)
Curr Opin Struct Biol
, vol.7
, pp. 194-199
-
-
Moult, J.1
-
29
-
-
84986512474
-
Charmm: A program for macromolecu]ar energy, minimization, and dynamics calculations
-
Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. Charmm: a program for macromolecu]ar energy, minimization, and dynamics calculations. J Comput Chem 1983;4:187-217.
-
(1983)
J Comput Chem
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
30
-
-
0032561237
-
Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
-
Duan Y, Kollman PA. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution [see comments]. Science 1998;282:740-744.
-
(1998)
Science
, vol.282
, pp. 740-744
-
-
Duan, Y.1
Kollman, P.A.2
-
31
-
-
0001064488
-
Statistical potentials extracted from protein structures: Are these meaningful potentials?
-
Ben-Naim A. Statistical potentials extracted from protein structures: are these meaningful potentials? J Chem Phys 1997;107:3698-3706.
-
(1997)
J Chem Phys
, vol.107
, pp. 3698-3706
-
-
Ben-Naim, A.1
-
32
-
-
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
-
34
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul SF, Madden TL, Schaffer AA, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25:3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
-
36
-
-
0024544755
-
A fast and sensitive multiple sequence alignment algorithm
-
Vingron M, Argos P. A fast and sensitive multiple sequence alignment algorithm. Comput Appl Biosci 1989;5:115-121.
-
(1989)
Comput Appl Biosci
, vol.5
, pp. 115-121
-
-
Vingron, M.1
Argos, P.2
-
37
-
-
0029011701
-
A 2nd generation force-field for the simulation of proteins, nucleic-acids, and organic-molecules
-
Cornell WD, Cieplak P, Bayly CI, et al. A 2nd 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
-
38
-
-
33846823909
-
Particle mesh Ewald: An N. log(N) method for Ewald sums in large systems
-
Darden T, York D, Pedersen L. Particle mesh Ewald: an N. log(N) method for Ewald sums in large systems. J Chem Phys 1993;98:10089-10092.
-
(1993)
J Chem Phys
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
39
-
-
33646940952
-
Numerical integration of the Cartesian equations of motion with contraints: Molecular dynamics of n-alkanes
-
Ryckaert J, Ciccotti G, Berendsen H. Numerical integration of the Cartesian equations of motion with contraints: molecular dynamics of n-alkanes. J Comput Phys 1977;23:327-341.
-
(1977)
J Comput Phys
, vol.23
, pp. 327-341
-
-
Ryckaert, J.1
Ciccotti, G.2
Berendsen, H.3
-
40
-
-
33750587438
-
-
Berendsen H, Postma J, van Gunsteren W, DiNola J, Haak J. J Chem Phys 1984;81:3684.
-
(1984)
J Chem Phys
, vol.81
, pp. 3684
-
-
Berendsen, H.1
Postma, J.2
Van Gunsteren, W.3
DiNola, J.4
Haak, J.5
-
41
-
-
0032553332
-
Elucidating the folding problem of alpha-helices: Local motifs, long-range electrostatics, ionic-strength dependence and prediction of NMR parameters
-
Lacroix E, Viguera AR, Serrano L. Elucidating the folding problem of alpha-helices: local motifs, long-range electrostatics, ionic-strength dependence and prediction of NMR parameters. J Mol Biol 1998;284:173-191.
-
(1998)
J Mol Biol
, vol.284
, pp. 173-191
-
-
Lacroix, E.1
Viguera, A.R.2
Serrano, L.3
-
42
-
-
0027972206
-
Dynamics in rugged energy landscapes with applications to the S-peptide and ribonuclease-A
-
Straub JE, Rashkin AB, Thirumalai D. Dynamics in rugged energy landscapes with applications to the S-peptide and ribonuclease-A. J Am Chem Soc 1994;116:2049-2063.
-
(1994)
J Am Chem Soc
, vol.116
, pp. 2049-2063
-
-
Straub, J.E.1
Rashkin, A.B.2
Thirumalai, D.3
-
44
-
-
0035008585
-
Energy landscape of a peptide consisting of alpha-helix, 3(10)-helix, beta-turn, beta-hairpin, and other disordered conformations
-
Higo J, Ito N, Kuroda M, Ono S, Nakajima N, Nakamura H. Energy landscape of a peptide consisting of alpha-helix, 3(10)-helix, beta-turn, beta-hairpin, and other disordered conformations. Protein Sci 2001;10:1160-1171.
-
(2001)
Protein Sci
, vol.10
, pp. 1160-1171
-
-
Higo, J.1
Ito, N.2
Kuroda, M.3
Ono, S.4
Nakajima, N.5
Nakamura, H.6
-
45
-
-
0036467163
-
Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics
-
Sanbonmatsu KY, Garcia AE. Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics. Proteins 2002;46:225-234.
-
(2002)
Proteins
, vol.46
, pp. 225-234
-
-
Sanbonmatsu, K.Y.1
Garcia, A.E.2
-
46
-
-
0015859467
-
Principles that govern the folding of protein chains
-
Anfinsen CB. Principles that govern the folding of protein chains. Science 1973;181:223-230.
-
(1973)
Science
, vol.181
, pp. 223-230
-
-
Anfinsen, C.B.1
|