Provides tools and data to build and perform RNA knowledge-based molecular simulations and tests.
This project is made of three parts. It first contains a collection of RNA Replica-Exchange Molecular Dynamics generated decoys to test RNA force-fields and simulation methodology. The second part is made by a collection of MD program input files to perform minimization and/or molecular dynamics simulation with the knowledge-based force field we developed. Available as Gromacs4 files for the moment, both all-atom and coarse-grained simulation are possible.
The last part is a database from which the filtered non-redundant dataset extracted for building the knowledge-based potential can be browsed and queried.
Decoy structures, KB potential and MD simulation setup are avaiable in the download section.