An embedded work-flow, integrated documentation and visualization tools shorten the number of steps to follow, starting from calculations to result visualization. Several scripts from the tool suites were updated and new ones were also added and integrated with 2D/3D visualization via the web interface. The server simplifies the set-up required for running these tools and visualizing their results. This may lead to the discovery of key residues involved in biological processes, such as drug resistance. Typically, following molecular dynamic simulations designed to investigate intrinsic and extrinsic protein perturbations (for instance induced by allosteric and orthosteric ligands, protein binding, temperature, pH and mutations), this selection of tools can be used to further describe protein dynamics.
Altogether, these tools allow for the exploration of protein dynamics at various levels of detail, spanning single residue perturbations and weighted contact network representations, to global residue centrality measurements and the investigation of global protein motion.
LINE 6 HELIX SERVER MODE SOFTWARE
The web server, MDM-TASK-web, combines the MD-TASK and MODE-TASK software suites, which are aimed at the coarse-grained analysis of static and all-atom MD-simulated proteins, using a variety of non-conventional approaches, such as dynamic residue network analysis, perturbation-response scanning, dynamic cross-correlation, essential dynamics and normal mode analysis.
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