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 […]
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MDAnalysis
MDAnalysis documentation¶ Release: 0.19.2 Date: Nov 08, 2018 MDAnalysis (www.mdanalysis.org) is an object-oriented python toolkit to analyze molecular dynamics trajectories generated by CHARMM, Gromacs, Amber, NAMD, LAMMPS, DL_POLY and other packages; it also reads other formats (e.g., PDB files and XYZ format trajectories; see Table of supported coordinate formats and Table of Supported Topology Formats for the full lists). It can write most of these formats, too, together with atom selections […]
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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 […]