TransAtlas:

TransAtlas Results

Once a particular conformational transition has been found and selected from the search section, TransAtlas web interface shows the information available for the simulation in a graphical way, divided in four different sections:

The first tab (Summary) gives an overview of the trajectory information from 4 different points of view: Protein Sequence & Structures information, Conformational Transition Simulation parameters and download options, Conformational Transition Simulation Descriptors, and Conformational Transition Simulation Family to easily find similar conformational transitions using the TransAtlas Ontology. The second tab (Visualization), gives a graphical view of the conformational transition thanks to the JSMol visualizer. On top of the trajectory representation, the TransAtlas Visualization section allows the possibility to label the different Collective Variables identified in the development of the database, as well as the different moving parts present in the structure, and the set of residue contacts formed, broken and transient during the conformational transition. The third tab (Atomistic Analysis), adds to the power of the TransAtlas database the possibility to work with a set of intermediate structures along the conformational transition in an atomistic resolution. Atomistic Molecular Dynamics thanks to the link with MDWeb server, or Biased MD thanks to the plumed configuration files automaticaly generated by the server are two different options offered in this section of the web server. And finally, the fourth tab (Links), is linking the particular conformational transition structures (PDBs) to a set of web servers designed and developed in the Molecular Modeling and Bioinformatics group, to further study flexibility information (FlexServ, MoDEL), find out information about the structures (PDB) or even compute atomistic Molecular Dynamics simulations (MDWeb).