Wojciech K. Kasprzak (pr. Voytek Casp-shack)
Bioinformatics Analyst Programmer
Basic Science Program
Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute
Leidos Biomedical Research, Inc.
Utilizing resources of the Bioinformatics and Computational Science program: BACS
In support of:
RNA Biology Laboratory (RNABL)
RNA Structure and Design Section
National Cancer Institute at Frederick
Bldg 560, Rm 11-82
Frederick, MD 21702
USA
Phone: 301 846 5537
email: wojciech.kasprzak@nih.gov
Professional Society memberships: Biophysical Society, The RNA Society, International Society of RNA Nanotechnology and Nanomedicine
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 fully 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 database 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.
- Design and characterization of RNA-based nano-scale structures and other RNA 3D modeling - see the featured stories in CCR Connection and CCR In the Journals, and watch our video on Designing RNA Nanoscaffolds to Deliver Drugs.
- Utilization of our Massively Parallel Genetic Algorithm MPGAfold 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).
- StructureLab - a heterogeneous computing environment workbench for multifaceted RNA structure prediction and analysis.