-
1
-
-
36749042541
-
Critical assessment of methods of protein structure prediction-round vii
-
Moult,J., Fidelis,K., Kryshtafovych,A., Rost,B., Hubbard,T. and Tramontano,A. (2007) Critical assessment of methods of protein structure prediction-round vii. Proteins, 69 (Suppl. 8), 3-9.
-
(2007)
Proteins
, vol.69
, Issue.SUPPL. 8
, pp. 3-9
-
-
Moult, J.1
Fidelis, K.2
Kryshtafovych, A.3
Rost, B.4
Hubbard, T.5
Tramontano, A.6
-
2
-
-
55249086989
-
The construction of a bioactive peptide database in metazoa
-
Liu,F., Baggerman,G., Schoofs,L. and Wets,G. (2008) The construction of a bioactive peptide database in metazoa. J. Proteome Res., 7 4119-4131.
-
(2008)
J. Proteome Res
, vol.7
, pp. 4119-4131
-
-
Liu, F.1
Baggerman, G.2
Schoofs, L.3
Wets, G.4
-
3
-
-
0031062621
-
Two-dimensional 1h NMR experiments show that the 23-residue magainin antibiotic peptide is an alpha-helix in dodecylphosphocholine micelles sodium dodecylsulfate micelles, and trifluoroethanol/water solution
-
Gesell,J., Zasloff,M. and Opella,S.J. (1997) Two-dimensional 1h NMR experiments show that the 23-residue magainin antibiotic peptide is an alpha-helix in dodecylphosphocholine micelles sodium dodecylsulfate micelles, and trifluoroethanol/water solution. J. Biomol. NMR, 9, 127-135.
-
(1997)
J. Biomol. NMR
, vol.9
, pp. 127-135
-
-
Gesell, J.1
Zasloff, M.2
Opella, S.J.3
-
4
-
-
0036264457
-
Mini-proteins trp the light fantastic
-
Gellman,S.H. and Woolfson,D.N. (2002) Mini-proteins trp the light fantastic. Nat. Struct. Biol., 9, 408-410.
-
(2002)
Nat. Struct. Biol
, vol.9
, pp. 408-410
-
-
Gellman, S.H.1
Woolfson, D.N.2
-
5
-
-
2642670311
-
Design of a 20-amino acid, three-stranded beta-sheet protein
-
Kortemme,T., Ramírez-Alvarado,M. and Serrano,L. (1998) Design of a 20-amino acid, three-stranded beta-sheet protein. Science, 281 253-256.
-
(1998)
Science
, vol.281
, pp. 253-256
-
-
Kortemme, T.1
Ramírez-Alvarado, M.2
Serrano, L.3
-
6
-
-
0036499409
-
Folding and stability of the three-stranded beta-sheet peptide betanova: Insights from molecular dynamics simulations
-
Colombo,G., Roccatano,D. and Mark,A.E. (2002) Folding and stability of the three-stranded beta-sheet peptide betanova: Insights from molecular dynamics simulations. Proteins, 46, 380-392.
-
(2002)
Proteins
, vol.46
, pp. 380-392
-
-
Colombo, G.1
Roccatano, D.2
Mark, A.E.3
-
7
-
-
10744226366
-
Rosetta predictions in casp5: Successes, failures, and prospects for complete automation
-
Bradley,P., Chivian,D., Meiler,J., Misura,K.M.S., Rohl,C.A., Schief,W.R., Wedemeyer,W.J., Schueler-Furman,O., Murphy,P., Schonbrun,J. et al. (2003) Rosetta predictions in casp5: Successes, failures, and prospects for complete automation. Proteins, 53 (Suppl 6) 457-468.
-
(2003)
Proteins
, vol.53
, Issue.SUPPL. 6
, pp. 457-468
-
-
Bradley, P.1
Chivian, D.2
Meiler, J.3
Misura, K.M.S.4
Rohl, C.A.5
Schief, W.R.6
Wedemeyer, W.J.7
Schueler-Furman, O.8
Murphy, P.9
Schonbrun, J.10
-
8
-
-
0037042264
-
Molecular dynamics study of peptides in implicit water: Ab initio folding of beta-hairpin, beta-sheet, and beta beta alpha-motif
-
Jang,S., Shin,S. and Pak,Y. (2002) Molecular dynamics study of peptides in implicit water: Ab initio folding of beta-hairpin, beta-sheet, and beta beta alpha-motif. J. Am. Chem. Soc., 124, 4976-4977.
-
(2002)
J. Am. Chem. Soc
, vol.124
, pp. 4976-4977
-
-
Jang, S.1
Shin, S.2
Pak, Y.3
-
9
-
-
61749091340
-
Replica exchange molecular dynamics simulations of coarse-grained proteins in implicit solvent
-
Chebaro,Y., Dong,X., Laghaei,R., Derreumaux,P. and Mousseau,N. (2009) Replica exchange molecular dynamics simulations of coarse-grained proteins in implicit solvent. J. Phys. Chem. B., 113, 267-274.
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 267-274
-
-
Chebaro, Y.1
Dong, X.2
Laghaei, R.3
Derreumaux, P.4
Mousseau, N.5
-
10
-
-
0001170125
-
A diffusion process-controlled Monte Carlo method for finding the global energy minimum of a polypeptide chain. i. formulation and test on a hexadecapeptide
-
Derreumaux,P. (1997) A diffusion process-controlled Monte Carlo method for finding the global energy minimum of a polypeptide chain. i. formulation and test on a hexadecapeptide. J. Chem. Phys., 106 5260-5270.
-
(1997)
J. Chem. Phys
, vol.106
, pp. 5260-5270
-
-
Derreumaux, P.1
-
11
-
-
0032917636
-
Predicting the structures of 18 peptides using geocore
-
Ishikawa,K., Yue,K. and Dill,K.A. (1999) Predicting the structures of 18 peptides using geocore. Protein Sci., 8, 716-721.
-
(1999)
Protein Sci
, vol.8
, pp. 716-721
-
-
Ishikawa, K.1
Yue, K.2
Dill, K.A.3
-
12
-
-
34548684339
-
Pepstr: A de novo method for tertiary structure prediction of small bioactive peptides
-
Kaur,H., Garg,A. and Raghava,G.P.S. (2007) Pepstr: A de novo method for tertiary structure prediction of small bioactive peptides. Protein Pept. Lett., 14, 626-631.
-
(2007)
Protein Pept. Lett
, vol.14
, pp. 626-631
-
-
Kaur, H.1
Garg, A.2
Raghava, G.P.S.3
-
13
-
-
33751081825
-
Prediction of peptide structure: How far are we?
-
Thomas,A., Deshayes,S., Decaffmeyer,M., Van Eyck,M.H., Charloteaux,B. and Brasseur,R. (2006) Prediction of peptide structure: How far are we? Proteins, 65, 889-897.
-
(2006)
Proteins
, vol.65
, pp. 889-897
-
-
Thomas, A.1
Deshayes, S.2
Decaffmeyer, M.3
Van Eyck, M.H.4
Charloteaux, B.5
Brasseur, R.6
-
14
-
-
58149293686
-
Generalized pattern search algorithm for peptide structure prediction
-
Nicosia,G. and Stracquadanio,G. (2008) Generalized pattern search algorithm for peptide structure prediction. Biophys. J., 95, 4988-4999.
-
(2008)
Biophys. J
, vol.95
, pp. 4988-4999
-
-
Nicosia, G.1
Stracquadanio, G.2
-
15
-
-
2442592993
-
A hidden Markov model derived structural alphabet for proteins
-
Camproux,A.C., Gautier,R. and Tufféry,P. (2004) A hidden Markov model derived structural alphabet for proteins. J. Mol. Biol., 339 591-605.
-
(2004)
J. Mol. Biol
, vol.339
, pp. 591-605
-
-
Camproux, A.C.1
Gautier, R.2
Tufféry, P.3
-
16
-
-
16244378861
-
Improved greedy algorithm for protein structure reconstruction
-
Tuffery,P., Guyon,F. and Derreumaux,P. (2005) Improved greedy algorithm for protein structure reconstruction. J. Comput. Chem., 26, 506-513.
-
(2005)
J. Comput. Chem
, vol.26
, pp. 506-513
-
-
Tuffery, P.1
Guyon, F.2
Derreumaux, P.3
-
17
-
-
28644449215
-
Dependency between consecutive local conformations helps assemble protein structures from secondary structures using go potential and greedy algorithm
-
Tuffery,P. and Derreumaux,P. (2005) Dependency between consecutive local conformations helps assemble protein structures from secondary structures using go potential and greedy algorithm. Proteins, 61, 732-740.
-
(2005)
Proteins
, vol.61
, pp. 732-740
-
-
Tuffery, P.1
Derreumaux, P.2
-
18
-
-
34548809141
-
A coarse-grained protein force field for folding and structure prediction
-
Maupetit,J., Tuffery,P. and Derreumaux,P. (2007) A coarse-grained protein force field for folding and structure prediction. Proteins 69, 394-408.
-
(2007)
Proteins
, vol.69
, pp. 394-408
-
-
Maupetit, J.1
Tuffery, P.2
Derreumaux, P.3
-
19
-
-
0030801002
-
Gapped blast and psi-blast: A new generation of protein database search programs
-
Altschul,S.F., Madden,T.L., Schäffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped blast and psi-blast: A new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schäffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
20
-
-
34347388470
-
Uniref: Comprehensive and non-redundant uniprot reference clusters
-
Suzek,B.E., Huang,H., McGarvey,P., Mazumder,R. and Wu,C.H. (2007) Uniref: Comprehensive and non-redundant uniprot reference clusters. Bioinformatics, 23, 1282-1288.
-
(2007)
Bioinformatics
, vol.23
, pp. 1282-1288
-
-
Suzek, B.E.1
Huang, H.2
McGarvey, P.3
Mazumder, R.4
Wu, C.H.5
-
21
-
-
0033578684
-
Protein secondary structure prediction based on position-specific scoring matrices
-
Jones,D.T. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol., 292, 195-202.
-
(1999)
J. Mol. Biol
, vol.292
, pp. 195-202
-
-
Jones, D.T.1
-
22
-
-
33846234246
-
Coarse-grained protein molecular dynamics simulations
-
Derreumaux,P. and Mousseau,N. (2007) Coarse-grained protein molecular dynamics simulations. J. Chem. Phys., 126, 025101.
-
(2007)
J. Chem. Phys
, vol.126
, pp. 025101
-
-
Derreumaux, P.1
Mousseau, N.2
-
23
-
-
33747819887
-
Sabbac: Online structural alphabet-based protein backbone reconstruction from alpha-carbon trace
-
Maupetit,J., Gautier,R. and Tufféry,P. (2006) Sabbac: Online structural alphabet-based protein backbone reconstruction from alpha-carbon trace. Nucleic Acids Res., 34, W147-W151.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Maupetit, J.1
Gautier, R.2
Tufféry, P.3
-
24
-
-
27344454932
-
Gromacs: Fast, flexible, and free
-
Van Der Spoel,D., Lindahl,E., Hess,B., Groenhof,G., Mark,A.E. and Berendsen,H.J.C. (2005) Gromacs: Fast, flexible, and free. J. Comput. Chem., 26, 1701-1718.
-
(2005)
J. Comput. Chem
, vol.26
, pp. 1701-1718
-
-
Van Der Spoel, D.1
Lindahl, E.2
Hess, B.3
Groenhof, G.4
Mark, A.E.5
Berendsen, H.J.C.6
-
25
-
-
0042622381
-
Lga: A method for finding 3d similarities in protein structures
-
Zemla,A. (2003) Lga: A method for finding 3d similarities in protein structures. Nucleic Acids Res., 31, 3370-3374.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3370-3374
-
-
Zemla, A.1
-
26
-
-
10344232638
-
Scoring function for automated assessment of protein structure template quality
-
Zhang,Y. and Skolnick,J. (2004) Scoring function for automated assessment of protein structure template quality. Proteins, 57 702-710.
-
(2004)
Proteins
, vol.57
, pp. 702-710
-
-
Zhang, Y.1
Skolnick, J.2
-
27
-
-
4143145167
-
10 residue folded peptide designed by segment statistics
-
Honda,S., Yamasaki,K., Sawada,Y. and Morii,H. (2004) 10 residue folded peptide designed by segment statistics. Structure, 12, 1507-1518.
-
(2004)
Structure
, vol.12
, pp. 1507-1518
-
-
Honda, S.1
Yamasaki, K.2
Sawada, Y.3
Morii, H.4
-
28
-
-
0023875642
-
A two-dimensional NMR study of the antimicrobial peptide magainin 2
-
Marion,D., Zasloff,M. and Bax,A. (1988) A two-dimensional NMR study of the antimicrobial peptide magainin 2. FEBS Lett., 227, 21-26.
-
(1988)
FEBS Lett
, vol.227
, pp. 21-26
-
-
Marion, D.1
Zasloff, M.2
Bax, A.3
-
29
-
-
0029619259
-
Knowledge-based protein secondary structure assignment
-
Frishman,D. and Argos,P. (1995) Knowledge-based protein secondary structure assignment. Proteins, 23, 566-579.
-
(1995)
Proteins
, vol.23
, pp. 566-579
-
-
Frishman, D.1
Argos, P.2
|