Computational biophysics software

We are also quite interested in many other biologically important systems such as viral capsid assembly. In order to understand the fundamentals and mechanisms of biological processes, proper tools are highly demanded. We develop novel computational software and packages to model and simulate biological systems. These tools are developed to s…. Molecular motors such as kinesin and dynein transport cargos along microtubules in the cell.

Dysfunction of molecular motors leads to many serious diseases. Several computational approaches are developed and applied to study the molecula…. Senior Investigator. Meet the Team. Contact us. Research Interests Research Interests. Projects Molecular Dynamics Simulations of Biological Macromolecules Molecular dynamics simulations are used to predict or explain function or structures of peptides and proteins and their substrates. Development of Theoretical Methods for Studying Biological Macromolecules New theoretical techniques are developed and characterized.

These efforts are usually coupled with software development, and involve the systematic testing and evaluation of new ideas.

Three-dimensional Structures of Biological Macromolecule We use computational techniques with experimental data to determine the three-dimensional structures of biological macromolecules and molecular assemblies. Experimental techniques include electron microscopy, electron tomography, NMR spectroscopy, and CD spectroscopy.

Development of Advance Computer Hardware and Software We develop and refine parallel computing techniques for macromolecular simulation and build suitable hardware required to efficiently execute it. Lab Group The Laboratory of Computational Biophysics is a group of researchers who use high-performance computing to investigate molecular dynamics. Featured Publications A protocol for preparing explicitly solvated systems for stable molecular dynamics simulations. Read Publication.

We also rely extensively on the nation's supercomputers. The TCB Group is also dedicated to helping both the biomedical community, and the computational world as a whole, by sharing the knowledge developed while administering the group internally. This knowledge is shared in the user and sysadmin documentation libraries. Addititionally, source code can be found as part of the MDTools library. VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

NAMD, recipient of a Gordon Bell Award , is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.

You can build NAMD yourself or download binaries for a wide variety of platforms.