TransAtlas:

TransAtlas Search

The main functionality of TransAtlas web interface is the possibility to query our Database of Conformational Transitions. The easiest and quickest way to access a particular conformational transition is searching from a PDB code. To do that, a Quick Search function is always visible at the top-right part of the menu bar:

TransAtlas Search section is divided in four tabs:

Conformational Transitions can be searched directly from the reference and target PDB codes (e.g. 1ake_A to 4ake_B), from a single PDB code, from a particular Uniprot Code or from a FASTA sequence in the Search Tab from the TransAtlas Search section. Advanced search queries to find conformational transitions from a set of different simulation descriptors as Root Mean Square deviations, Radius of Gyration, Collectivity Index or number of Broken/Formed/Transient contacts (see Descriptors section), can be made in the Advanced Search Tab from the TransAtlas Search section. The complete list of Conformational Transitions stored in our database can be browsed in the Browse Tab from the TransAtlas Search section. TransAtlas database can be browsed from our own Transition Movements Ontology, and from the Protein Structure Classification CATH folds. Results from the previous queries or browse sections are shown in the Results Tab from the TransAtlas Search section. Similar conformational transitions are grouped together in clusters (see references). Once a particular conformational transition is chosen, information about the simulation will be opened in the next TransAtlas section: TransAtlas.