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Adapting Scientific Software and Designing Algorithms for Next Generation GPU Computing Platforms
ver_ http://www.ks.uiuc.edu/Research/gpu/files/siam2019-softnextgenplatforms-stone.pdf
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RMSD analysis of trajectory (DCD file) using VMD
Mohamed shehata This video shows you how to calculate the RMSD analysis of aa protein using the software VMD from the University of Illinois (http://www.ks.uiuc.edu/). VMD is a powerful tool for analysis of structures and trajectories. Numerous tools for analysis are available under the VMD Main menu item Extensions $ \rightarrow $ Analysis. In addition […]
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Locating Binding Sites in Protein Structures
Paul Labute and Martin SantavyChemical Computing Group Inc.Introduction | Methodology | Results | Summary | References Introduction Active sites in proteins are usually hydrophobic pockets that involve sidechain atoms. It is non-trivial to quantify this rule of thumb. Methods such as [Goodford 1985] or [Miranker 1991] use interaction energies between the receptor and different probes in an […]