Enabling Large-Scale Biomolecular Conformation Search with Replica Exchange Statistical Temperature Molecular Dynamics (RESTMD) over HPC and Cloud Computing Resources
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Wei Huang | Seung-Jong Park | Chris Knight | Joohyun Kim | Richard Platania | Nayong Kim | Tom Keyes | Wei Huang | Nayong Kim | Richard Platania | Christopher Knight | Tom Keyes | Seung-Jong Park | Joohyun Kim
[1] U. Hansmann. Parallel tempering algorithm for conformational studies of biological molecules , 1997, physics/9710041.
[2] Alexander D. MacKerell,et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.
[3] Y. Sugita,et al. Replica-exchange molecular dynamics method for protein folding , 1999 .
[4] D. Landau,et al. Efficient, multiple-range random walk algorithm to calculate the density of states. , 2000, Physical review letters.
[5] P. Wolynes. Landscapes, funnels, glasses, and folding: from metaphor to software , 2001 .
[6] K. Tai. Conformational sampling for the impatient. , 2004, Biophysical chemistry.
[7] J. Karn,et al. Structure-based drug design targeting an inactive RNA conformation: exploiting the flexibility of HIV-1 TAR RNA. , 2004, Journal of molecular biology.
[8] J. Straub,et al. Statistical-temperature Monte Carlo and molecular dynamics algorithms. , 2006, Physical review letters.
[9] J. Straub,et al. Statistical temperature molecular dynamics: application to coarse-grained beta-barrel-forming protein models. , 2007, The Journal of chemical physics.
[10] A. Liwo,et al. Computational techniques for efficient conformational sampling of proteins. , 2008, Current opinion in structural biology.
[11] Joohyun Kim,et al. All-atom molecular dynamics simulations of beta-hairpins stabilized by a tight turn: pronounced heterogeneous folding pathways. , 2010, The journal of physical chemistry. B.
[12] J. Straub,et al. Replica exchange statistical temperature molecular dynamics algorithm. , 2012, The journal of physical chemistry. B.
[13] Christoph Junghans,et al. Molecular Dynamics in the Multicanonical Ensemble: Equivalence of Wang-Landau Sampling, Statistical Temperature Molecular Dynamics, and Metadynamics. , 2014, Journal of chemical theory and computation.
[14] Seung-Jong Park,et al. MapReduce-Based RESTMD: Enabling Large-Scale Sampling Tasks with Distributed HPC Systems , 2014, 2014 6th International Workshop on Science Gateways.