RNA-structure dynamics explored with full atom, explicit solvent Molecular Dynamics and coarse-grained methods, such as the Anisotropic Network Model, a form of Elastic Network Model.
Prediction and MD-based characterization of small ligands docking to RNA.
RNA Junction Database
- a databas of 3D RNA junctions extracted from PDB entries for the
purpose of RNA nanostructure design. All the junctions have been
subjected to energy minimization in Amber (reaching nearest local
minimum), and their RMSD relative to the initial structure and the
minimized 3D coordinates are also available.
Utilization of our Massively Parallel Genetic AlgorithmMPGAfold
to determine multiple functional structures (states) of RNA sequences, such as those we have shown for the HDV Type III (with differences for the strains from Ecuador and Peru), HIV 5'UTR, hok/sok and pstvd systems (see publications).
You can download binaries of our many software packages
for Linux (and PC/Mac) platforms.
Here is a PubMed
search of my publications (journal papers; several are not available via PubMed),
and here is my short Resume and my CV with full bibliography (all papers, book chapters and presentations) as of September, 2019.