메뉴 건너뛰기




Volumn 78, Issue 6, 2010, Pages 1583-1593

Feature space resampling for protein conformational search

Author keywords

Ab initio; Feature selection; Folding; Machine learning; Rosetta

Indexed keywords

ACCURACY; ARTICLE; GENETIC ALGORITHM; GENETIC RECOMBINATION; MOLECULAR MODEL; MONTE CARLO METHOD; PREDICTION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

EID: 77951224747     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22677     Document Type: Article
Times cited : (15)

References (22)
  • 1
    • 50649095790 scopus 로고    scopus 로고
    • Macromolecular modeling with Rosetta
    • Das R, Baker D. Macromolecular modeling with Rosetta. Ann Rev Biochem 2008;77:362-382.
    • (2008) Ann Rev Biochem , vol.77 , pp. 362-382
    • Das, R.1    Baker, D.2
  • 2
    • 0001176785 scopus 로고    scopus 로고
    • New optimization method for conformational energy calculations on polypeptides: Conformational space annealing
    • Lee J, Scheraga HA, Rackovsky S. New optimization method for conformational energy calculations on polypeptides: conformational space annealing. J Comput Chem 1997;18:1222-1232. (Pubitemid 127650577)
    • (1997) Journal of Computational Chemistry , vol.18 , Issue.9 , pp. 1222-1232
    • Lee, J.1    Scheraga, H.A.2    Rackovsky, S.3
  • 3
    • 29144515725 scopus 로고    scopus 로고
    • Improving protein structure prediction with model-based search
    • Brunette TJ, Brock O. Improving protein structure prediction with model-based search. Bioinformatics 2005;21 (Suppl l):66-74.
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. L , pp. 66-74
    • Brunette, T.J.1    Brock, O.2
  • 4
    • 0002363078 scopus 로고
    • On the experimental attainment of optimum conditions (with discussion)
    • Box GEP, Wilson KB. On the experimental attainment of optimum conditions (with discussion). J Royal Stat Soc Series B 1951;13:1-45.
    • (1951) J Royal Stat Soc Series B , vol.13 , pp. 1-45
    • Box, G.E.P.1    Wilson, K.B.2
  • 5
    • 24044449704 scopus 로고    scopus 로고
    • Learning evaluation functions to improve optimization by local search
    • Boyan J, Moore AW. Learning evaluation functions to improve optimization by local search. J Mach Learn Res 2001;1:77-112. (Pubitemid 33738777)
    • (2001) Journal of Machine Learning Research , vol.1 , Issue.2 , pp. 108-112
    • Boyan, J.A.1    Moore, A.W.2
  • 6
    • 0026448484 scopus 로고
    • Potential of genetic algorithms in protein folding and protein engineering simulations
    • Dandekar T, Argos P. Potential of genetic algorithms in protein folding and protein engineering simulations. Protein Eng 1992;5:637-645.
    • (1992) Protein Eng , vol.5 , pp. 637-645
    • Dandekar, T.1    Argos, P.2
  • 7
    • 0028865590 scopus 로고
    • Ab initio structure prediction for small polypeptides and protein fragments using genetic algorithms
    • Pedersen JT, Moult J. Ab initio structure prediction for small polypeptides and protein fragments using genetic algorithms. Proteins 1995;23:454-460.
    • (1995) Proteins , vol.23 , pp. 454-460
    • Pedersen, J.T.1    Moult, J.2
  • 8
    • 0009636533 scopus 로고    scopus 로고
    • Protein folding simulation with genetic algorithm and supersecondary structure constraints
    • DOI 10.1002/(SICI)1097-0134(19980515)31:3<247::AID-PROT2>3.0.CO;2-G
    • Cui Y, Chen RS, Wong WH. Protein folding simulation with genetic algorithm and super-secondary structure constraints. Proteins 1998;31:247-257. (Pubitemid 28217813)
    • (1998) Proteins: Structure, Function and Genetics , vol.31 , Issue.3 , pp. 247-257
    • Cui, Y.1    Chen, R.S.2    Wong, W.H.3
  • 9
    • 0030819348 scopus 로고    scopus 로고
    • Muiticanonicai ensemble generated by molecular dynamics simulation for enhanced conformational sampling of peptides
    • Nakajima N, Nakamura H, Kidera A. Muiticanonicai ensemble generated by molecular dynamics simulation for enhanced conformational sampling of peptides J Phys Chem B 1997;101:817-824.
    • (1997) J Phys Chem B , vol.101 , pp. 817-824
    • Nakajima, N.1    Nakamura, H.2    Kidera, A.3
  • 10
    • 58149299971 scopus 로고    scopus 로고
    • Metadynamics: A method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science
    • 22pp
    • Laio A, Gervasio FL. Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science. Reports Prog Phys 2008;71:126601 (22pp).
    • (2008) Reports Prog Phys , vol.71 , pp. 126601
    • Laio, A.1    Gervasio, F.L.2
  • 11
    • 6644221271 scopus 로고    scopus 로고
    • Efficient, multiple-range random walk algorithm to calculate the density of states
    • Wang F, Landau DP. Efficient, multiple-range random walk algorithm to calculate the density of states. Phys Rev Lett 2001;86:2050.
    • (2001) Phys Rev Lett , vol.86 , pp. 2050
    • Wang, F.1    Landau, D.P.2
  • 12
    • 70349241497 scopus 로고    scopus 로고
    • Sampling bottlenecks in de novo protein structure prediction
    • Kim DE, Blum B, Bradley P, Baker D. Sampling bottlenecks in de novo protein structure prediction. J Mol Biol 2009;393:249-260.
    • (2009) J Mol Biol , vol.393 , pp. 249-260
    • Kim, D.E.1    Blum, B.2    Bradley, P.3    Baker, D.4
  • 13
    • 0032502839 scopus 로고    scopus 로고
    • Contact order, transition state placement and the refolding rates of single domain proteins
    • DOI 10.1006/jmbi.1998.1645
    • Plaxco KW, Simons KT, Baker D. Contact order, transition state placement and the refolding rates of single domain proteins. J Mol Biol 1998;277:985-994. (Pubitemid 28195995)
    • (1998) Journal of Molecular Biology , vol.277 , Issue.4 , pp. 985-994
    • Plaxco, K.W.1    Simons, K.T.2    Baker, D.3
  • 14
    • 77958398767 scopus 로고
    • The convergence of a class of double-rank minimization algorithms
    • Broyden CG. The convergence of a class of double-rank minimization algorithms. J Inst Math Appl 1970;6:76-90.
    • (1970) J Inst Math Appl , vol.6 , pp. 76-90
    • Broyden, C.G.1
  • 15
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • DOI 10.1006/jmbi.1999.3091
    • Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999;292:195-202. (Pubitemid 29435759)
    • (1999) Journal of Molecular Biology , vol.292 , Issue.2 , pp. 195-202
    • Jones, D.T.1
  • 16
    • 0035789525 scopus 로고    scopus 로고
    • Generation and evaluation of dimension-reduced amino acid parameter representations by artificial neural networks
    • DOI 10.1007/s008940100038
    • Meiler J, Müller M, Zeidler A, Schmäschke F. Generation and evaluation of dimension-reduced amino acid parameter representations by artificial neural networks. J Mol Model 2001;7:360-369. (Pubitemid 36153544)
    • (2001) Journal of Molecular Modeling , vol.7 , Issue.9 , pp. 360-369
    • Meiler, J.1    Muller, M.2    Zeidler, A.3    Schmaschke, F.4
  • 17
    • 0032438987 scopus 로고    scopus 로고
    • Hidden Markov models for detecting remote protein homologies
    • DOI 10.1093/bioinformatics/14.10.846
    • Karplus K, Barrett C, Hughey R. Hidden Markov models for detecting remote protein homologies. Bioinformatics 1998;14:846-856. (Pubitemid 29041540)
    • (1998) Bioinformatics , vol.14 , Issue.10 , pp. 846-856
    • Karplus, K.1    Barrett, C.2    Hughey, R.3
  • 18
    • 33751118503 scopus 로고    scopus 로고
    • Improved beta-protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation
    • DOI 10.1002/prot.21133
    • Bradley P, Baker D. Improved beta-protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation. Proteins 2006;65:922-929. (Pubitemid 44772890)
    • (2006) Proteins: Structure, Function and Genetics , vol.65 , Issue.4 , pp. 922-929
    • Bradley, P.1    Baker, D.2
  • 22
    • 7444236378 scopus 로고    scopus 로고
    • Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation
    • DOI 10.1073/pnas.0404703101
    • Qian B, Ortiz AR, Baiter D. Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation. Proc Natl Acad Sci USA 2004;101: .15346-15351. (Pubitemid 39441544)
    • (2004) Proceedings of the National Academy of Sciences of the United States of America , vol.101 , Issue.43 , pp. 15346-15351
    • Qian, B.1    Ortiz, A.R.2    Baker, D.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.