메뉴 건너뛰기




Volumn 57, Issue 2, 2004, Pages 338-344

Significance of conformational biases in Monte Carlo simulations of protein folding: Lessons from Metropolis-Hastings approach

Author keywords

Biased sampling; Detailed balance principle; Hierarchical folding; Metropolis Hasting algorithm; Minimalist models; Protein folding

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; ANALYTIC METHOD; ARTICLE; ENERGY; EXPERIMENTAL MODEL; MATHEMATICAL ANALYSIS; METROPOLIS HASTINGS ALGORITHM; MONTE CARLO METHOD; PREDICTION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN TERTIARY STRUCTURE;

EID: 4544278435     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20210     Document Type: Article
Times cited : (6)

References (23)
  • 4
    • 0142116211 scopus 로고    scopus 로고
    • A reversible fragment assembly method for de novo structure prediction
    • Chikenji G, Fujitsuka Y, Takada S. A reversible fragment assembly method for de novo structure prediction. J Chem Phys 2003;119: 6895-6903.
    • (2003) J Chem Phys , vol.119 , pp. 6895-6903
    • Chikenji, G.1    Fujitsuka, Y.2    Takada, S.3
  • 6
    • 0242267506 scopus 로고    scopus 로고
    • Prediction of protein structure by emphasizing local side-chain/backbone in ensembles of turn fragments
    • Fang Q, Shortle D. Prediction of protein structure by emphasizing local side-chain/backbone in ensembles of turn fragments. Proteins 2003;53:486-490.
    • (2003) Proteins , vol.53 , pp. 486-490
    • Fang, Q.1    Shortle, D.2
  • 7
    • 0037398844 scopus 로고    scopus 로고
    • Minimalist models for protein folding and design
    • Head-Gordon T, Brown S. Minimalist models for protein folding and design. Curr Opin in Struc Biol 2003;12:160-167.
    • (2003) Curr Opin in Struc Biol , vol.12 , pp. 160-167
    • Head-Gordon, T.1    Brown, S.2
  • 8
    • 0000019986 scopus 로고
    • Protein folding as a stochastic process
    • Go N. Protein folding as a stochastic process. J Stat Physics 1983:413-423.
    • (1983) J Stat Physics , pp. 413-423
    • Go, N.1
  • 9
    • 77956890234 scopus 로고
    • Monte Carlo sampling methods using Markov chains and their applications
    • Hastings WK. Monte Carlo sampling methods using Markov chains and their applications. Biometrika 1970;57:97-109.
    • (1970) Biometrika , vol.57 , pp. 97-109
    • Hastings, W.K.1
  • 10
    • 0028149160 scopus 로고
    • Exploring conformational space with a simple lattice model for protein structure
    • Hinds DA, Levitt M. Exploring conformational space with a simple lattice model for protein structure. J Mol Biol 1994;243(4): 668-82.
    • (1994) J Mol Biol , vol.243 , Issue.4 , pp. 668-682
    • Hinds, D.A.1    Levitt, M.2
  • 11
    • 1842500993 scopus 로고    scopus 로고
    • Unfolded state of polyalanine is a segmented polyproline II helix
    • In press
    • Kentsis, A., Mezei, M., Gindin, T. and Osman, R. Unfolded state of polyalanine is a segmented polyproline II helix. Proteins 2004; In press.
    • (2004) Proteins
    • Kentsis, A.1    Mezei, M.2    Gindin, T.3    Osman, R.4
  • 14
    • 1842500992 scopus 로고    scopus 로고
    • Polyproline II helix is the preferred conformation for unfolded polyalanine in water
    • In press
    • Mezei M, Fleming PJ, Srinivasan R, Rose GD. Polyproline II helix is the preferred conformation for unfolded polyalanine in water. Proteins 2004; In press.
    • (2004) Proteins
    • Mezei, M.1    Fleming, P.J.2    Srinivasan, R.3    Rose, G.D.4
  • 15
    • 0018782641 scopus 로고
    • Hierarchic organization of domains in globular proteins
    • Rose GD. Hierarchic organization of domains in globular proteins. J Mol Biol 1979;134:447-470.
    • (1979) J Mol Biol , vol.134 , pp. 447-470
    • Rose, G.D.1
  • 16
    • 0037143694 scopus 로고    scopus 로고
    • The ensemble folding kinetics of protein G from all-atom Monte Carlo simulation
    • Shimada J, Shakhnovich EI. The ensemble folding kinetics of protein G from all-atom Monte Carlo simulation. Proc Natl Acad Sci USA 2002;99:11175-11180.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 11175-11180
    • Shimada, J.1    Shakhnovich, E.I.2
  • 17
    • 0035919635 scopus 로고    scopus 로고
    • Persistence of native-like topology in a denaturated protein in 8M urea
    • Shorle D., Ackerman MS. Persistence of native-like topology in a denaturated protein in 8M urea. Science 2001;293:487-489.
    • (2001) Science , vol.293 , pp. 487-489
    • Shorle, D.1    Ackerman, M.S.2
  • 18
    • 0029000696 scopus 로고
    • Knowledge-based potentials for proteins
    • Sippl MJ. Knowledge-based potentials for proteins. Curr Opin Struc Biol 1995;5:229-35.
    • (1995) Curr Opin Struc Biol , vol.5 , pp. 229-235
    • Sippl, M.J.1
  • 19
    • 0025784650 scopus 로고
    • Dynamic Monte Carlo simulations of a new lattice model of globular protein folding, structure and dynamics
    • Skolnick J, Kolinski A. Dynamic Monte Carlo simulations of a new lattice model of globular protein folding, structure and dynamics. J Mol Biol 1991;221(2):499-531.
    • (1991) J Mol Biol , vol.221 , Issue.2 , pp. 499-531
    • Skolnick, J.1    Kolinski, A.2
  • 20
    • 0029055313 scopus 로고
    • LINUS - A hierarchical procedure to predict the fold of a protein
    • Srinivasan R., Rose GD. LINUS - a hierarchical procedure to predict the fold of a protein. Prot 1995;22(2):81-99.
    • (1995) Prot , vol.22 , Issue.2 , pp. 81-99
    • Srinivasan, R.1    Rose, G.D.2
  • 21
    • 0033405203 scopus 로고    scopus 로고
    • A physical basis for protein secondary structure
    • Srinivasan R, Rose GD. A physical basis for protein secondary structure. Proc Nat Acad Sci USA 1999;96(25):14258-14263.
    • (1999) Proc Nat Acad Sci USA , vol.96 , Issue.25 , pp. 14258-14263
    • Srinivasan, R.1    Rose, G.D.2
  • 22
    • 0036606453 scopus 로고    scopus 로고
    • Ab initio prediction of protein structure using LINUS
    • Srinivasan R., Rose G.D. Ab initio prediction of protein structure using LINUS. Prot 2002;47(4):489-495.
    • (2002) Prot , vol.47 , Issue.4 , pp. 489-495
    • Srinivasan, R.1    Rose, G.D.2
  • 23
    • 0030048675 scopus 로고    scopus 로고
    • Folding proteins with a simple energy function and extensive conformational searching
    • Yue K, Dill KA. Folding proteins with a simple energy function and extensive conformational searching. Prot Sci 1996;5:254-261.
    • (1996) Prot Sci , vol.5 , pp. 254-261
    • Yue, K.1    Dill, K.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.