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Issue No.02 - March/April (2012 vol.9)
pp: 476-486
Yi-Ming Cheng , Dept. of Biochem. & Mol. Biol., Michigan State Univ., East Lansing, MI, USA
S. M. Gopal , Dept. of Biochem. & Mol. Biol., Michigan State Univ., East Lansing, MI, USA
S. M. Law , Dept. of Biochem. & Mol. Biol., Michigan State Univ., East Lansing, MI, USA
M. Feig , Dept. of Biochem. & Mol. Biol., Chem., & Comput. Sci. & Eng., Michigan State Univ., East Lansing, MI, USA
ABSTRACT
Molecular dynamics trajectories are very data intensive thereby limiting sharing and archival of such data. One possible solution is compression of trajectory data. Here, trajectory compression based on conversion to the coarse-grained model PRIMO is proposed. The compressed data are about one third of the original data and fast decompression is possible with an analytical reconstruction procedure from PRIMO to all-atom representations. This protocol largely preserves structural features and to a more limited extent also energetic features of the original trajectory.
INDEX TERMS
Trajectory, Accuracy, Protocols, Biological system modeling, Computational modeling, Solvents, Proteins,coarse-grained model., Proteins, all-atom reconstruction, PRIMO, molecular dynamics simulation, compression
CITATION
Yi-Ming Cheng, S. M. Gopal, S. M. Law, M. Feig, "Molecular Dynamics Trajectory Compression with a Coarse-Grained Model", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.9, no. 2, pp. 476-486, March/April 2012, doi:10.1109/TCBB.2011.141
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