TimeScapes is an analysis package that can be used to efficiently detect and characterize significant conformational changes in simulated biomolecular systems. The program makes use of a particular type of “coarse-grained” model to reduce the level of detail in the spatial representations of long MD trajectories. TimeScapes decomposes structural changes into a set of key side-chain motions, providing greater sensitivity to a wide range of significant conformational changes than is typically obtained from traditional RMSD-based metrics.
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J Chem Theory Comput. 2009 Oct 13;5(10):2595-605. doi: 10.1021/ct900229u.
Automated Event Detection and Activity Monitoring in Long Molecular Dynamics Simulations.
Wriggers W, Stafford KA, Shan Y, Piana S, Maragakis P, Lindorff-Larsen K, Miller PJ1, Gullingsrud J, Rendleman CA, Eastwood MP, Dror RO, Shaw DE.