메뉴 건너뛰기




Volumn 9, Issue 8, 2013, Pages 3816-3825

Sampling of protein folding transitions: Multicanonical versus replica exchange molecular dynamics

Author keywords

[No Author keywords available]

Indexed keywords


EID: 84882443100     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct400312d     Document Type: Article
Times cited : (18)

References (29)
  • 1
    • 0030516672 scopus 로고    scopus 로고
    • Exchange Monte Carlo Method and Applications to Spin Glass Simulations
    • Hukushima, K.; Nemoto, K. Exchange Monte Carlo Method and Applications to Spin Glass Simulations J. Phys. Soc. (Japan) 1996, 65, 1604-1608
    • (1996) J. Phys. Soc. (Japan) , vol.65 , pp. 1604-1608
    • Hukushima, K.1    Nemoto, K.2
  • 2
    • 84950437936 scopus 로고
    • Annealing Markov Chain Monte Carlo with Applications to Ancestral Inference
    • Geyer, G. J.; Thompson, E. A. Annealing Markov Chain Monte Carlo with Applications to Ancestral Inference J. Am. Stat. Assn. 1995, 90 (431) 909-920
    • (1995) J. Am. Stat. Assn. , vol.90 , Issue.431 , pp. 909-920
    • Geyer, G.J.1    Thompson, E.A.2
  • 3
    • 35949020425 scopus 로고
    • Replica Monte Carlo Simulation of Spin-Glasses
    • Swendsen, R.; Wang, J. Replica Monte Carlo Simulation of Spin-Glasses Phys. Rev. Lett. 1986, 57, 2607-2609
    • (1986) Phys. Rev. Lett. , vol.57 , pp. 2607-2609
    • Swendsen, R.1    Wang, J.2
  • 4
    • 0031578972 scopus 로고    scopus 로고
    • Parallel Tempering Algorithm for Conformational Studies of Biological Molecules
    • Hansmann, U. H. E. Parallel Tempering Algorithm for Conformational Studies of Biological Molecules Chem. Phys. Lett. 1997, 281, 140-150
    • (1997) Chem. Phys. Lett. , vol.281 , pp. 140-150
    • Hansmann, U.H.E.1
  • 5
    • 0000106469 scopus 로고
    • Multicanonical Algorithms for First Order Phase Transitions
    • Berg, B.; Neuhaus, T. Multicanonical Algorithms for First Order Phase Transitions Phys. Lett. B 1991, 267, 249-253
    • (1991) Phys. Lett. B , vol.267 , pp. 249-253
    • Berg, B.1    Neuhaus, T.2
  • 6
    • 5244260010 scopus 로고
    • Prediction of Peptide Conformation by Multicanonical Algorithm: A New Approach to the Multiple-Minima Problem
    • Hansmann, U. H. E.; Okamoto, Y. Prediction of Peptide Conformation by Multicanonical Algorithm: A New Approach to the Multiple-Minima Problem J. Comput. Chem. 1993, 14, 1333-1338
    • (1993) J. Comput. Chem. , vol.14 , pp. 1333-1338
    • Hansmann, U.H.E.1    Okamoto, Y.2
  • 7
    • 0030572603 scopus 로고    scopus 로고
    • Molecular Dynamics, Langevin and Hydrid Monte Carlo Simulations in a Multicanonical Ensemble
    • Hansmann, U. H. E.; Okamoto, Y.; Eisenmenger, F. Molecular Dynamics, Langevin and Hydrid Monte Carlo Simulations in a Multicanonical Ensemble Chem. Phys. Lett. 1996, 259, 321-330
    • (1996) Chem. Phys. Lett. , vol.259 , pp. 321-330
    • Hansmann, U.H.E.1    Okamoto, Y.2    Eisenmenger, F.3
  • 8
    • 0030819348 scopus 로고    scopus 로고
    • Multicanonical Ensemble Generated by Molecular Dynamics Simulation for Enhanced Conformational Sampling of Peptides
    • Nakajima, N.; Nakamura, H.; Kidera, A. Multicanonical Ensemble Generated by Molecular Dynamics Simulation for Enhanced Conformational Sampling of Peptides J. Phys. Chem. 1997, 101, 817-824
    • (1997) J. Phys. Chem. , vol.101 , pp. 817-824
    • Nakajima, N.1    Nakamura, H.2    Kidera, A.3
  • 9
    • 0942277678 scopus 로고    scopus 로고
    • Folding Simulations of the Parathyroid Hormon Fragment (1-34)
    • Hansmann, U. H. E. Folding Simulations of the Parathyroid Hormon Fragment (1-34) J. Chem. Phys. 2004, 120, 417-422
    • (2004) J. Chem. Phys. , vol.120 , pp. 417-422
    • Hansmann, U.H.E.1
  • 10
    • 33644850613 scopus 로고    scopus 로고
    • The Investigation of the Secondary Structure of Various Peptide Sequences of β-Casein by Molecular Modeling
    • Yaşar, F.; Çelik, S.; Köksel, H. The Investigation of the Secondary Structure of Various Peptide Sequences of β-Casein by Molecular Modeling Phys. A 2006, 363, 348-358
    • (2006) Phys. A , vol.363 , pp. 348-358
    • Yaşar, F.1    Çelik, S.2    Köksel, H.3
  • 11
    • 0033687195 scopus 로고    scopus 로고
    • Helix-Coil Transitions of Amino Acid Homo-oligomers in Aqueous Solution Studied by Multicanonical Simulations
    • Mitsutake, A.; Okamoto, Y. Helix-Coil Transitions of Amino Acid Homo-oligomers in Aqueous Solution Studied by Multicanonical Simulations J. Chem. Phys. 2000, 112, 10638-10647
    • (2000) J. Chem. Phys. , vol.112 , pp. 10638-10647
    • Mitsutake, A.1    Okamoto, Y.2
  • 12
    • 40149099893 scopus 로고    scopus 로고
    • Thermodynamics of Peptide Aggregation Processes. An Analysis from Perspectives of Three Statistical Ensembles
    • Junghans, C.; Bachmann, M.; W. Janke, W. Thermodynamics of Peptide Aggregation Processes. An Analysis from Perspectives of Three Statistical Ensembles J. Chem. Phys. 2008, 128, 085103
    • (2008) J. Chem. Phys. , vol.128 , pp. 085103
    • Junghans, C.1    Bachmann, M.2    Janke W, W.3
  • 13
    • 56649095574 scopus 로고    scopus 로고
    • Microcanonical Analyses of Homopolymer Aggregation Processes
    • Chen, T.; Lin, X. S.; Liu, Y.; Lu, T.; Liang, H. J. Microcanonical Analyses of Homopolymer Aggregation Processes Phys. Rev. E 2008, 78, 056101
    • (2008) Phys. Rev. e , vol.78 , pp. 056101
    • Chen, T.1    Lin, X.S.2    Liu, Y.3    Lu, T.4    Liang, H.J.5
  • 14
    • 84877320154 scopus 로고    scopus 로고
    • Multicanonical Simulation of Biomolecules and Microcanonical Statistical Analysis of Conformational Transitions
    • Bachmann, M. Multicanonical Simulation of Biomolecules and Microcanonical Statistical Analysis of Conformational Transitions Phys. Scr. 2013, 87, 058504
    • (2013) Phys. Scr. , vol.87 , pp. 058504
    • Bachmann, M.1
  • 15
    • 84867442920 scopus 로고    scopus 로고
    • Enhanced and Effective Conformational Sampling of Protein Molecular Systems for Their Free Energy Landscapes
    • Higo, J.; Ikebe, J.; Kamiya, N.; Nakamura, H. Enhanced and Effective Conformational Sampling of Protein Molecular Systems for Their Free Energy Landscapes Biophys. Rev. 2012, 4, 27-44
    • (2012) Biophys. Rev. , vol.4 , pp. 27-44
    • Higo, J.1    Ikebe, J.2    Kamiya, N.3    Nakamura, H.4
  • 16
    • 63449135082 scopus 로고    scopus 로고
    • An All-Atom Structure-Based Potential for Proteins: Bridging Minimal Models with All-Atom Empirical Forcefields
    • Whitford, P.; Noel, J.; Gosavi, S.; Schug, A.; Sanbonmatsu, K.; Onuchic, J. An All-Atom Structure-Based Potential for Proteins: Bridging Minimal Models with All-Atom Empirical Forcefields Proteins 2009, 75, 430-441
    • (2009) Proteins , vol.75 , pp. 430-441
    • Whitford, P.1    Noel, J.2    Gosavi, S.3    Schug, A.4    Sanbonmatsu, K.5    Onuchic, J.6
  • 17
    • 84862167431 scopus 로고    scopus 로고
    • Modeling Structural Flexibility of Proteins with Go-Models
    • Jiang, P.; Hansmann, U. H. E. Modeling Structural Flexibility of Proteins with Go-Models J. Chem. Theory Comput. 2012, 8, 2127-2133
    • (2012) J. Chem. Theory Comput. , vol.8 , pp. 2127-2133
    • Jiang, P.1    Hansmann, U.H.E.2
  • 18
    • 41349094233 scopus 로고    scopus 로고
    • Optimizing the Ensemble for Equilibration in Broad-Histogram Monte Carlo Simulations
    • Trebst, S.; Huse, D.; Troyer, M. Optimizing the Ensemble for Equilibration in Broad-Histogram Monte Carlo Simulations Phys. Rev. E 2004, 70, 046701-046705
    • (2004) Phys. Rev. e , vol.70 , pp. 046701-046705
    • Trebst, S.1    Huse, D.2    Troyer, M.3
  • 20
    • 77049109643 scopus 로고    scopus 로고
    • Folding Simulations of a de Novo Designed Protein with a βαβ Fold
    • Qi, Y.; Huang, Y.; Liang, H.; Liu, Z.; Lai, L. Folding Simulations of a De Novo Designed Protein with a βαβ Fold Biophys. J. 2010, 98, 321-329
    • (2010) Biophys. J. , vol.98 , pp. 321-329
    • Qi, Y.1    Huang, Y.2    Liang, H.3    Liu, Z.4    Lai, L.5
  • 21
    • 46249092554 scopus 로고    scopus 로고
    • Gromacs 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
    • Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. Gromacs 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation J. Chem. Theory Comput. 2008, 4, 435-447
    • (2008) J. Chem. Theory Comput. , vol.4 , pp. 435-447
    • Hess, B.1    Kutzner, C.2    Van Der Spoel, D.3    Lindahl, E.4
  • 22
    • 38749123962 scopus 로고    scopus 로고
    • P-Lincs: A Parallel Linear Constraint Solver for Molecular Simulation
    • Hess, B. P-Lincs: A Parallel Linear Constraint Solver for Molecular Simulation J. Chem. Theory Comput. 2008, 4, 116-122
    • (2008) J. Chem. Theory Comput. , vol.4 , pp. 116-122
    • Hess, B.1
  • 23
    • 34547809547 scopus 로고
    • A Unified Formulation of the Constant Temperature Molecular Dynamics Methods
    • Nose, S. A Unified Formulation of the Constant Temperature Molecular Dynamics Methods J. Chem. Phys. 1984, 81, 511-519
    • (1984) J. Chem. Phys. , vol.81 , pp. 511-519
    • Nose, S.1
  • 24
    • 0027446365 scopus 로고
    • Isolation of a Candidate Gene for Menkes Disease and Evidence that It Encodes a Copper-Transporting ATPase
    • Vulpe, C.; Levinson, B.; Whitney, S.; Packman, S.; Gitschier, J. Isolation of a Candidate Gene for Menkes Disease and Evidence that It Encodes a Copper-Transporting ATPase Nat. Genet. 1993, 3, 7-13
    • (1993) Nat. Genet. , vol.3 , pp. 7-13
    • Vulpe, C.1    Levinson, B.2    Whitney, S.3    Packman, S.4    Gitschier, J.5
  • 25
    • 70449931860 scopus 로고    scopus 로고
    • Robustness and Generalization of Structure-Based Models for Protein Folding and Function
    • Lammert, H.; Schug, A.; Onuchic, J. Robustness and Generalization of Structure-Based Models for Protein Folding and Function Proteins 2009, 77, 881-891
    • (2009) Proteins , vol.77 , pp. 881-891
    • Lammert, H.1    Schug, A.2    Onuchic, J.3
  • 26
    • 77954276842 scopus 로고    scopus 로고
    • Smog@ctbp: Simplified Deployment of Structure-Based Models in Gromacs
    • Noel, J.; Whitford, P.; Sanbonmatsu, K.; Onuchic, J. Smog@ctbp: Simplified Deployment of Structure-Based Models in Gromacs Nucleic Acids Res. 2010, 38, 657-661
    • (2010) Nucleic Acids Res. , vol.38 , pp. 657-661
    • Noel, J.1    Whitford, P.2    Sanbonmatsu, K.3    Onuchic, J.4
  • 27
    • 34547139358 scopus 로고    scopus 로고
    • Optimized Parallel Tempering Simulations of Proteins
    • Trebst, S.; Troyer, M.; Hansmann, U. H. E. Optimized Parallel Tempering Simulations of Proteins J. Chem. Phys. 2006, 124, 174903
    • (2006) J. Chem. Phys. , vol.124 , pp. 174903
    • Trebst, S.1    Troyer, M.2    Hansmann, U.H.E.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.