BIGNASim database structure and analysis portal for nucleic acids simulation data
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DNA & RNA Structure and Helical Parameters Analyses (NAFlex)
----Tutorial 2 -- Global analysis (XCGY)
Tutorial 3 -- Meta-trajectory (XCGY)
Tutorial 4 -- Experimental vs MD analysis
----Tutorial 3: Meta-trajectories (XCGY)
This tutorial shows how to build a meta-trajectory containing a particular nucleotidic fragment with BIGNASim portal. For this tutorial, we will continue with the real example presented in the previous global analyses tutorial: CG base-pair step and the influence of the tetranucleotide environment in the sequence-dependent polymorphism of particular base-pair steps (P. Dans et al, NAR 2014). We have seen in the previous tutorial how to extract directly from the database the population of a particular helical parameter, recovering the Twist bimodality found in the above mentioned research. However, one can be interested in study different properties, not stored in BIGNASim database. For that, there is a possibility to generate and download (and also send to NAFlex server) a meta-trajectory containing just the nucleotide fragment of interest. It is build joining together the atomic information (3D cartesian coordinates) from all the simulations stored in our database enclosing the fragment. To illustrate the power of BIGNASim database, we interrogated the DB searching for the 16 possible different tetramers including CG base-pair, and we obtained results for all of them, going from 2 (TCGG) to 49 (TCGC) occurrences. We must say that for now, BIGNASim is populated with just a set of trajectories generated during the development and validation of the parmBSC1 force-field, and the information stored is going to be increased with new simulations.