TransAtlas:

TransAtlas Links Tab

The particular conformational transition selected in the TransAtlas Search section is split into the initial reference and target structures used to compute the simulation; these structures are then linked to 4 different web servers related to protein structure information, dynamics and flexibilty:

• MMB PDB Mirror
• Molecular Dynamics Extended Library (MoDEL)
• Molecular Dynamics on Web (MDWeb)
• Flexibility Server (FlexServ)

Protein Data Bank MMB Mirror

Experimental information about the PDB structures (reference and target) can be graphically obtained using the Molecular Modelling and Bioinformatics PDB mirror. Information available from this website is: different chains forming the molecule, their sequences and cluster families linked to uniprot database; PDB structure and biounit files in PDB, mmCIF and json format; PDB structure interactive visualization with JSMol. Moreover, this website is linked to all the molecular dynamics structural databases generated by the group: MoDEL for protein simulations, BigNASim for nucleic acids simulations.

Molecular Dynamics Extended Library (MoDEL)

Molecular Dynamics Extended Library (MoDEL) database contains ~2000 different atomistic Molecular Dynamics simulations of protein structures. MoDEL web server presents them together with a set of analysis and information associated.

Molecular Dynamics on Web (MDWeb)

Molecular Dynamics on Web (MDWeb) is a web server to setup atomistic Molecular Dynamics simulations. It offers services to setup the systems for the most widely-used molecular dynamics packages (Gromacs, Amber and Namd). TranAtlas is directly linked to MDWeb as the proteins used to compute the conformational transition (reference and target) are directly uploaded to MDWeb so that the user can easily start working on the protein system setup. MDWeb is also directly linked to TransAtlas in the Atomistic Models analysis section, where all of the generated intermediate atomistic frames are coupled to MDWeb to easily start an MD setup and eventually a MD simulation with them.

Flexibility Server (FlexServ)

Protein Flexibility Server (FlexServ) is a web server that gathers together a set of protein flexibility analysis, either from Coarse-Grained simulated trajectories and also from atomistic MD trajectories. The list of flexibility analysis are: RMSd, B-factors, Apparent stiffness, chained correlations, Principal Component Analysis, collectivity indexes, hinge predictions, lindemann coefficients, and more (see FlexServ). The conformational transition trajectory computed in TransAtlas is directly uploaded into FlexServ, so that the flexibility analysis set included in the server could be directly computed.