TransAtlas:

TransAtlas Presentation

We present TransAtlas: Atlas of Protein Conformational Transitions, the first proteome-scale database of conformational transitions in proteins. Using a novel CG approach (Sfriso et al., 2013) powered by a discrete molecular dynamics (dMD) algorithm we explored 750K conformational transitions (63646 of which are unique) deriving 7.5M intermediate snapshots with Cα resolution. From these paths we extracted detailed biophysical information that was used to rationalize and classify the protein motion, as well as to derive a robust set of collective variables (CVs) capturing the conformational change, and that can be used in biased simulations. The Cα-resolution transition intermediate snapshots were projected to the atomistic detail, generating input files using MDWeb (MDWeb) for atomistic MD simulations (either unbiased and biased). TransAtlas web interface allows to browse the resulting Database, search for a particular protein, visualize the conformational transition, and work with (or download) the intermediate atomistic structures generated. These help pages show what TransAtlas web interface offer, going section by section. To start using TransAtlas, please continue with the Getting Started page.