TransAtlas:

TransAtlas Atomistic Analysis Tab

The Cα-resolution intermediate structures visited along the transition path were modelled back into the atomistic level using MODELLER to rebuild the side chains. Up to 8.1 M atomistic intermediate structures for all transitions are stored in TransAtlas database, and available to download and/or work with them from this section of the web server. Models can directly be used, for instance in preliminary docking experiments, or as starting point for MD simulations thanks to a tailored link to our MDWeb server, which provides the external user with solvated pre-equilibrated structures and topology files in for standard MD calculations.

TransAtlas Atomistic Analysis tab offers the reconstructed atomistic models for a chosen set of intermediate structures from the conformational transition. The number of intermediate structures depends on the complexity of the transition. Additionally, this section is meant to help running biased MD simulations using the rich information given by the conformational transition, such as Targeted MD (atomistic TMD, using an origin and a target structure chosen from the set of intermediate structures) or Path Collective Variable (using the whole set of intermediate structures from the conformational transition), using Plumed software. The TransAtlas Atomistic Analysis section can be divided in three different modules:

• Quality Control Box
• Atomistic Intermediate Structures
• Biased MD Simulations with Plumed

Quality Control Box

When working with atomistic structures, it is of crutial importance to start with correct structures. This "correctness" is achieved mainly if the structure is connected (not having missing parts). The Quality Control box, computed and shown for each of the conformational transition in TransAtlas (see Quality Control help section), easily gives the required information needed to decide if the structure can be directly used in an atomistic calculation, or if it would need some kind of pre-processing (usually residues addition).

Atomistic Intermediate Structures

The set of atomistic intermediate structures taken and reconstructed from the conformational transition are easily browsed, viewed and downloaded thanks to an embeded slider:

The slider lets move the origin and the target structure. Every time one of the two endpoints is changed, the boxes shown below the slider change accordingly. In these boxes, information such us the frame number and the difference between the chosen frames and the conformational transition origin and target structures (in RMSd) is shown, together with the possibility to view the structure with JSMol , download it , or send it to MDWeb server (see Atomistic MD Tutorial).

An additional box shows the difference (in RMSd) between the chosen frames (origin and target) together and lets the user visualize both of them together with JSMol, easying the selection process.

Finally, TransAtlas also gives the possibility to download all the reconstructed atomistic intermediate frames in different trajectory formats: ASCII crd, binaries Binpos, NetCDF and Gromacs TRR, and also as an ensemble of PDB files or a single multi-PDB file. The slider presented before is also connected to the next module of these section, the biased MD simulations. Origin and target structures chosen in the slider will be the ones used in the Targeted MD technique.

Biased MD Simulations with Plumed

The reconstructed atomistic frames from the conformational transitions can be used to run further atomistic biased MD simulations. Moreover, the collective variables extracted in TransAtlas database can then be used to track the transition with the generated biased trajectory.

TransAtlas biased MD simulation section is meant to help in using information extracted from the conformational transition with biased MD techniques implemented for example in Plumed software. TransAtlas recommends and presents two different biased techniques to further extend the information obtained in the Coarse-Grained simulations: Targeted MD and Path Collective Variables. Targeted MD: More information can be found in plumed help pages: Plumed Targeted MD Path Collective Variable: More information can be found in plumed help pages: Plumed Path Collective Variable