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

Abstract

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: http://polyview.cchmc.org/conform.html.

Figure 1.

Visualization of MD trajectory for resilin-like peptide with changes in SS states along the trajectory shown in (A). Red colors correspond to different helices, green to beta states and blue to unstructured regions, bends and magenta to turns, respectively (see POLYVIEW-MM documentation for details). Each row corresponds to an individual snapshot of the structure, an example of which is shown in (B) with tyrosine side chains shown in colors corresponding to initial SS states and using stick models. Note the lack of regular SSs.

Figure 2.

Analysis of docking models for the complex of fucose and norovirus capsid protein. Right panel shows alternative fucose poses superimposed together. The corresponding interaction interfaces are shown in the left upper panel, with residues in contact with the ligand indicated by magenta. In the lower left panel, amino acid residues are aligned with the corresponding profiles: evolutionary conservation, physico-chemical properties, SS and RSA states.