TransAtlas:

TransAtlas Results Tab

After either searching or browsing TransAtlas database, the set of Conformational Transitions found will be shown in the Results Tab of the Search Section:

A blue region in the top part of the section shows the type of query performed to obtain the results shown (from PDB Code, from Conformational Transition, from Sequence, from Browsing the DB, etc.) (see corresponding Help Search Section).

The list of results is presented in clusters of conformational transitions having the same type of movements (see TransAtlas Ontology). The number of different clusters found with the corresponding parameters searched are shown, together with the total number of simulations. For each of the clusters, an expandable box containing the list of transitions is generated. Once expanded, a representative simulation for the particular cluster is shown, together with the list of conformational transitions included in the cluster:

The number of conformational transitions within the cluster are divided in the ones including the searched parameters and all the rest of simulations, corresponding to similar trajectories in terms of movements. The latter ones are hidden by default, but can be expanded by clicking at the last table row, displaying a couple of green arrows:

For the representative trajectory, snapshots of the reference and target structures are shown, together with information about the simulation such as initial and final RMSd. A list of icons redirects to the TransAtlas section of the web interface, where an exhaustive list of information about the structures used in the simulation and about the simulation itself are presented, together with a trajectory visualization using JSMol, atomistic analysis from trajectory representative snapshots, and links to other flexibility servers (see corresponding Help TransAtlas Section). Information about icons meaning can be found in the corresponding Help Icons Section.

For the list of trajectories included in a particular cluster, initial and final RMSd is shown, together with links to the Summary, Atomistic Analysis and Links tabs of the TransAtlas section of the server (see corresponding Help TransAtlas Section).