TransAtlas:

TransAtlas Browse Tab

TransAtlas web interface offers the possibility to browse our database of conformational transitions from the Browse Tab of the Search Section. The library can be browsed either from CATH Protein Structure Classification Database folds or from our own hierarchy of Conformational Transitions Movements.

Browse by CATH fold

The collection of TransAtlas Conformational Transitions are classified according to their CATH Protein Classification Database fold. Starting from the 4 main groups defined in the Class level of the CATH database (Mainly Alpha, Mainly Beta, Alpha-Beta and Few Secondary Structures), the web interface allows to navigate through the second (Architecture) and third (Topology) levels of the CATH folds classification. After choosing (clicking) the three CATH levels, a set of PDB codes corresponding to this particular fold represented in our TransAtlas library will be shown. Each of these entries will be clickable, and the set of Conformational Transitions having the particular structure will be opened in the Results Tab of the Search Section.

Browse by Conformational Transition Ontology

TransAtlas web interface implements an in-house developed hierarchy, built upon a Conformational Transition Ontology. This TransAtlas Ontology is generated from the Simulation Descriptors presented in the Descriptors help section. These descriptors were used to organize protein structural changes in the first large-scale ontology of protein motions. To classify all the simulation computed in TransAtlas, a classification tree was trained using a set of manually classified transitions. The complete ontology can be browsed in the Ontology help section.

Screenshot owl viewer.

The first level of the ontology splits Conformational transitions from Structural fluctuations (those explained as oscillations around equilibrium conformation). The second-order division is between motions conserving (Block motions) or not (Rearrangements) the structural elements (domain, loop, α-helix, etc.) along the transition. The third division involves dissecting block motions into transitions generated by Domains or Local Motions. Thanks to this ontology and the automatic classification of all the trajectories computed in TransAtlas, it is possible to easily find similar conformational transitions just clicking at the lowest level in the Ontology tree associated to every entry.