Please, see my publications on PubMed
(several not available via PubMed),
my short resume, and my CV with full bibliography
(all publications and presentations) as of May, 2021.
Many of our software packages
are available as individual binaries or as pre-installed tools inside properly configured Virtual Machine archive files (Ubuntu and CentOS for VBox)
Reseach interests and ongoing projects:
Prediction and MD-based characterization of small ligands docking to RNA.
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.
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 energy minimized 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).