TransAtlas:

TransAtlas Quality Control

A battery of Quality Control chekcs were done to the whole TransAtlas database. That allowed us to exclude trivial or aberrant conformational changes from the database such as:

• Trajectories were dynamics were concentrated on the first 7 or last 7 residues.
• Trajectories were only 3 or less residues changed their position.
• Trajectories that broke a C_α-C_α pseudo-bond.
• Trajectories were no contact was formed nor broken during the simulation.

Additionaly, the quality of the retained trajectories was assessed and it is showed in a graphical diagram in each TransAtlas entry of the web server.

Checks done for all the trajectories are:

• Initial structure contain gaps in the sequence.
• Gaps in the sequence are located in between two independent moving parts.

With this QC checks, conformational changes occuring between disconnected structure elements or pairs of structures representing an unreliable conformational transition can be easily identified.

Apart from the Quality Control checks, a complexity scale was also derived for each of the conformational transitions based on the number of fragments that move in a conformational change.

The complexity descriptor was defined as the largest number of effective nodes tiered in the motion tree. In other words, it represents the number of sub-parts that move embedded (hierarchically) in larger parts. For example, a two domain open-close conformational transition is assigned a complexity of 1 (only one independent motion). However, if inside one of those domains a loop were also changing its conformation the assigned complexity would be 2 (one domain and one loop inside the same domain). No motions showed more than 9 moving parts; the scale ranges from 0 to 9, and it is represented in the web server with a progress bar. The colour code of the progress bar goes from red (complexity between 1 and 2) to orange (complexity between 3 and 7) to green (complexity between 8 and 9) with increasing complexity.

If no gaps in the sequence were found for the initial structure and the dynamics are connected (no gaps in between two independent moving parts), then the conformational transition was classified by being OK and is represented by a green tick: