POLYVIEW-MM: Web-based platform for animation and analysis of molecular simulations

Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA.
Nucleic Acids Research (Impact Factor: 9.11). 07/2010; 38(Web Server issue):W662-6. DOI: 10.1093/nar/gkq445
Source: PubMed


Molecular simulations offer important mechanistic and functional clues in studies of proteins and other macromolecules. However, interpreting the results of such simulations increasingly requires tools that can combine information from multiple structural databases and other web resources, and provide highly integrated and versatile analysis tools. Here, we present a new web server that integrates high-quality animation of molecular motion (MM) with structural and functional analysis of macromolecules. The new tool, dubbed POLYVIEW-MM, enables animation of trajectories generated by molecular dynamics and related simulation techniques, as well as visualization of alternative conformers, e.g. obtained as a result of protein structure prediction methods or small molecule docking. To facilitate structural analysis, POLYVIEW-MM combines interactive view and analysis of conformational changes using Jmol and its tailored extensions, publication quality animation using PyMol, and customizable 2D summary plots that provide an overview of MM, e.g. in terms of changes in secondary structure states and relative solvent accessibility of individual residues in proteins. Furthermore, POLYVIEW-MM integrates visualization with various structural annotations, including automated mapping of known inter-action sites from structural homologs, mapping of cavities and ligand binding sites, transmembrane regions and protein domains. URL:

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    • "Classification of secondary structure plays a vital role in the identification of stability for the 10 given protein [Trevino et al., 2007]. The STRIDE program was used for computing the 11 secondary structure distribution which was graphically viewed via Polyview-MM [Porollo, and 12 Meller, 2010]. STRIDE is a python scripted program, which utilizes knowledge-based algorithm 13 to give an optimized output after evaluating both the hydrogen bond energy and torsion angles of 14 the residues. "
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