TransAtlas:

TransAtlas Advanced Search Tab

TransAtlas web interface offers the possibility to query our database of conformational transitions from the Advanced Search Tab of the Search Section using the set of biophysical Simulation Descriptors derived to characterize in a simplified way protein transitions, for example:

• Root Mean Square deviations
• Radius of Gyration
• Radius of Gyration Ratio
• Number of Residues
• Ratio between the number of internal distances changing (+15%) in the transition
• Collectivity index
• Number of PLS components capturing > 95% of the variance

See the Descriptors Help section to find the whole collection of biophysical Simulation Descriptors used in TransAtlas DB together with a short description and their values range through their interquartile range.

TransAtlas advanced search allows to query our DB using particular values for each of the Simulation Descriptors presented before. For that, a slider range is associated to each of the descriptors, avoiding the need to identify individual minimum, maximum and appropriate increment values for each of the descriptors:

The range is hidden by default, it appears clicking on the icon. Every time a slider range is changed, TransAtlas advanced search page automatically recalculates the number of conformational transitions complying all the required parameters. This number is updated in the top-right part of the page:

This counter is a crutial part of the advanced search, as it will inform when trying to retrieve information for more than 1000 conformational transitions. In this case, TransAtlas web interface will show an error and will ask to reduce the number of simulations in the set. As TransAtlas interface is designed to show graphical information of all the conformational transitions queried, preparing and showing information for a set of more than 1000 trajectories is out of the scope of this server.

It is able to retreave information for up to 1000 conformational transitions at the same time, but the recommendation to have a smooth and quick response is to work with reduced sets of less than 100 simulations. In that case (< 100 simulations), the counter number will be coloured green, whereas when working with a number from 100 to 1000, the counter number will be coloured orange. In this last case, a warning will be launched informing about the time needed by the server to retrieve information for these high number of trajectories.

In summary, always take a look at the number counter on the top-right part of the advanced Search page. The colour of the number will be informing you if the resulting set is:

• Small enough to start the query and retrieve the results (green).
• Big but with the possibility to start the query and retrieve the results in minutes time (orange).
• Too big to start the query and retrieve the results (red).

Each of the Simulation Descriptors have a icon that can be clicked to obtain information about the biophysical descriptor:

The set of Conformational Transitions found in the final query will be presented in the Results Tab of TransAtlas Search Section.