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Molecular Simulation Volume 41, 2015 - Issue 10-12: Proceedings of the 3rd International Conference on Molecular Simulation
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Proceedings of the 3rd International Conference on Molecular Simulation

Conformational search simulations of Trp-cage using genetic crossover

Yoshitake SakaeDepartment of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi464-8602, JapanView further author information
,
Tomoyuki HiroyasuDepartment of Biomedical Information, Doshisha University, Kyotanabe, Kyoto610-0394, JapanView further author information
,
Mitsunori MikiDepartment of Intelligent Information Engineering and Sciences, Doshisha University, Kyotanabe, Kyoto610-0394, JapanView further author information
,
Katsuya IshiiInformation Technology Center, Nagoya University, Nagoya, Aichi464-8601, JapanView further author information
&
Yuko OkamotoDepartment of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi464-8602, Japan;Information Technology Center, Nagoya University, Nagoya, Aichi464-8601, Japan;Structural Biology Research Center, Graduate School of Science, Nagoya University, Nagoya, Aichi464-8602, Japan;Center for Computational Science, Graduate School of Engineering, Nagoya University, Nagoya, Aichi464-8603, JapanCorrespondence[email protected]
View further author information
Pages 1045-1049 | Received 13 Oct 2014, Accepted 03 Feb 2015, Published online: 19 May 2015

References

  • Mitsutake A, Sugita Y, Okamoto Y. Generalized-ensemble algorithms for molecular simulations of biopolymers. Biopolymers (Pept. Sci). 2001;60(2):96–123. doi:10.1002/1097-0282(2001)60:2 < 96:AID-BIP1007>3.0.CO;2-F.
  • Berg BA, Neuhaus T. Multicanonical algorithms for first order phase transitions. Phys. Lett. B. 1991;267(2):249–253. doi:10.1016/0370-2693(91)91256-U.
  • Berg BA, Neuhaus T. Multicanonical ensemble: a new approach to simulate first-order phase transitions. Phys. Rev. Lett. 1992;68(1):9–12. doi:10.1103/PhysRevLett.68.9.
  • Lyubartsev AP, Martsinovski AA, Shevkunov SV, Vorontsov-velyaminov PN. New approach to Monte Carlo calculation of the free energy: method of expanded ensembles. J. Chem. Phys. 1992;96(3):1776–1783. doi:10.1063/1.462133.
  • Marinari E, Parisi G. Simulated tempering: a new Monte Carlo scheme. Europhys. Lett. 1992;19(6):451–458. doi:10.1209/0295-5075/19/6/002.
  • Hukushima K, Nemoto K. Exchange Monte Carlo method and application to spin glass simulations. J. Phys. Soc. Jpn. 1996;65(6):1604–1608. doi:10.1143/JPSJ.65.1604.
  • Sugita Y, Okamoto Y. Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Lett. 1999;314:141–151.
  • Hiroyasu T, Miki M, Ogura M. Parallel simulated annealing using genetic crossover, Proceedings of the 44th Institute of Systems 2000. p. 113–114.
  • Hiroyasu T, Miki M, Ogura M, Okamoto Y. Examination of parallel simulated annealing using genetic crossover. J. IPS Jpn. 2002;43:70–79.
  • Hiroyasu T, Miki M, Ogura M, Aoi K, Yoshida T, Okamoto Y. Atom-level simulations of protein folding. Proceedings of the 7th World Multiconference on Systemics, Cybernetics and Informatics (SCI 2003). 2003. p. 117–122.
  • Sakae Y, Hiroyasu T, Miki M, Okamoto Y. Protein structure predictions by parallel simulated annealing molecular dynamics using genetic crossover. J. Comput. Chem. 2011;32(7):1353–1360. doi:10.1002/jcc.21716.
  • Kirkpatrick S, Gelatt CD Jr., Vecchi MP. Optimization by simulated annealing. Science. 1983;220(4598):671–680. doi:10.1126/science.220.4598.671.
  • Holland JH. Adaptation in natural and artificial systems. Ann Arbor, MI: University of Michigan Press; 1975.
  • Goldberg DE. Genetic algorithms in search, optimization, and machine learning. Reading: Addison-Wesley; 1989.
  • Sakae Y, Hiroyasu T, Miki M, Ishii K, Okamoto Y. A conformational search method for protein systems using genetic crossover and Metropolis criterion. J. Phys. Conf. Series. 2014;487:012003. doi:10.1088/1742-6596/487/1/012003.
  • Neidigh JW, Fesinmeyer RM, Andersen NH. Designing a 20-residue protein. Nature Struct. Biol. 2002;9(6):425–430. doi:10.1038/nsb798.
  • TINKER program package; software available at http://dasher.wustl.edu/tinker/.
  • Hoover WG. Canonical dynamics: equilibrium phase-space distributions. Phys. Rev. A. 1985;31(3):1695–1697. doi:10.1103/PhysRevA.31.1695.
  • Hornak V, Abel A, Okur R, Strockbine B, Roitberg A, Simmerling C. Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins. 2006;65(3):712–725. doi:10.1002/prot.21123.
  • Still WC, Tempczyk A, Hawley RC, Hendrickson T. Semianalytical treatment of solvation for molecular mechanics and dynamics. J. Am. Chem. Soc. 1990;112(16):6127–6129. doi:10.1021/ja00172a038.
  • Qiu D, Shenkin PS, Hollinger FP, Still WC. The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born Radii. J. Phys. Chem. A. 1997;101(16):3005–3014. doi:10.1021/jp961992r.
  • Mitsutake A, Sugita Y, Okamoto Y. Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of peptides. II. Application to a more complex system. J. Chem. Phys. 2003;118(14):6676–6688. doi:10.1063/1.1555849.

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