TransAtlas:

TransAtlas Summary Tab

The first tab of TransAtlas interface after selecting a particular simulation is the Summary tab. In this part of the server, different type of information related to the conformational transition is presented through four different sections:

• Protein Sequence & Structures Information
• Conformational Transition Simulation Information
• Conformational Transition Simulation Descriptors
• Conformational Transition Simulation Family

Protein Sequence & Structures Information

Information about the proteins structures used as a reference and target for the conformational transition simulation is presented in this section, together with their uniprot id. For each protein structure, its PDB code, short description (Header + Compound), experimental type and resolution, and ligands present in the structure are shown. Snapshots of the structures are represented in the top-right part of the section, together with the number of residues for each of them, and the number of common residues between both.

Just below the structure's snapshots, the Quality check validation of the simulation is shown in a small box. Validations include gaps in the structure, gaps in sequence located betweeen two independent moving parts, and the complexity of the conformational transition. More information about the Quality check can be found in the specific help section. Finally, an interactive graphical representation of both the reference and the target structure used for the conformational transition simulation can be launched clicking at the JSMol logo. This will open a new window where the two structures are superposed and represented one on top of the other in two different colours, to easily identify the differences between them. Moreover, the power of JSMol web visualizer allows different types of secondary structure representations (Cartoon, Backbone, CPK, Ball and Stick, Wireframe), different types of colouring methods (by secondary structure, by chain, by amino acid, etc.), and a large number of options accessible clicking at the mouse right button on top of the JSMol screen. More information about JSMol visualizer can be found here: JSMol web page. PDB codes and ligands codes are linked to the PDB-MMB web server to obtain more information about them.

Conformational Transition Simulation Information

Information about the conformational transition simulation can be found in this section of the web server. Such information is a brief summary of results obtained after the analysis of the final trajectory. This summary includes:

• Total Simulation time, in number of steps.
• Initial and Final RMSd between reference and target structures presented in the previous section.
• Collectivity index, a measure of how many atoms are affected by the conformational transition (from 0 to 1).
• Type and Subclass of the conformational transition, according to the TransAtlas Ontology of protein conformational transitions.
• Moving parts of the structure, identified from the conformational transition.
• Number of contacts broken, formed or transient found along the conformational transition simulation.

In addition to the information listed above, a set of downloadable items are represented with the icon. The residue numbers identifying the different moving parts of the structures, or the set of residues involved in contacts broken, formed, or transient during the simulation can be obtained in two separate files. In a yellow box at the left part of the section, two trajectories are also offered as downloadable files: the raw trajectory produced by the Coarse-grained method (see references), with 1000 snapshots, and a reduced trajectory, containing a set of 100 snapshots chosen as the most representative ones from the original 1000 included in the raw trajectory.

Conformational Transition Simulation Descriptors

Key structural features were extracted from each of the simulations computed in the TransAtlas database. These features were derived from a set of biophysical descriptors chosen to characterize types of protein transitions in a simplified way. The complete set of descriptors together with a short description can be found in the Simulation Descriptors section of the help pages. The set of values for each of the described descriptors computed for the particular trajectory are listed in this section.

These descriptors were then used to classify the trajectories computed in TransAtlas according to the designed ontology of protein conformational transitions (see Ontology help section.

Conformational Transition Simulation Family

All trajectories computed in TransAtlas were classified and grouped together in conformational transitions cluster families. This classification, following the ontology defined in the project, allows to easily find similar conformational transitions. The tree of types and subclasses (if any) for each of the trajectories is shown in this section:

Clicking on one of the branches of the tree will redirect to the TransAtlas Browse tab of the Search section, where all the simulations with similar type of conformational transitions will be listed.