The movie demonstrates how the once computationally-intensive Molecular Dynamics Flexible Fitting (MDFF) method can now be achieved on a desktop in a matter of minutes using the NAMD software. Depicted is an HIV inactivating protein (in purple) being morphed by MDFF towards a simulated EM density map (in green) derived from the same protein in a different state, taken from the PDB database. Taking advantage of NAMD and GPU computing, the MDFF simulation shown only took 10 minutes to finish on a desktop. The greater speed provided by NAMD stands to advance cryo-EM modeling using the MDFF method.

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Related papers:

David E. Tanner, Kwok-Yan Chan, James Phillips, and Klaus Schulten. Parallel generalized Born implicit solvent calculations with NAMD. Journal of Chemical Theory and Computation, 7:3635-3642, 2011. (PMC: 3222955)
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Leonardo G. Trabuco, Elizabeth Villa, Kakoli Mitra, Joachim Frank, and Klaus Schulten. Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. Structure, 16:673-683, 2008. (PMC: 2430731)
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