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., ( Leidos )

Utilizing resources of the
Advanced Biomedical Computing Center: ABCC

In support of:
RNA Biology Laboratory (RNABL)
RNA Structure and Design Section
National Cancer Institute at Frederick
Building 560, Rm 11-82
Frederick, MD 21702
USA

Phone: 301 846 5537
Fax: 301 846 6911
e-mail:kasprzaw@mail.nih.gov


Professional Society memberships: Biophysical Society, The RNA Society

Reseach interests and ongoing projects:
  • Design and characterization of RNA-based nano-scale structures and other RNA 3D modeling - see the featured stories in CCR Connections and CCR In the Journals. Watch our a video on the subject of Designing RNA Nanoscaffolds to Deliver Drugs.

  • 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 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 secondary structure prediction and analysis. You can download binaries of this software package for PC/Linux and SGI/Irix platforms.


Here is a PubMed search of my publications (journal papers; a few are not available via PubMed), and here is my CV with full bibliography (all papers, book chapters and presentations) as of September, 2018.

Frederick, Maryland, USA:

Last revision: Sep. 25, 2018 by kasprzaw@mail.nih.gov