Kavraki Lab
Physical and Biological Computing

We develop computational tools on high-performance systems to model protein structure and function, understand biomolecular interactions and help analyze, in the long run, the molecular machinery of the cell. We integrate sequence information with three-dimensional structural information to capture, represent and exploit relevant molecular motion. Of particular interest are the identification of three-dimensional functional motifs in protein databases, docking of flexible molecules to flexible receptors, computer-assisted drug discovery, the characterization and analysis of protein motion, protein folding, and the compact representation and understanding of structural changes in large biomolecular machines. We apply robotics and computational geometry methods to the above problems.

Current Research Projects:

• Protein Modeling

  • Molecular Representations, Kinematics and Related Problems
  • Multiscale representation of proteins

• Protein Motion

  • Sampling-Based Modeling of Equilibrium Fluctuations in Proteins
  • Nonlinear Dimensionality Reduction for the Analysis of Protein Motion

• Protein Function

  • Functional Annotation of Proteins
  • Biomolecular Interactions and Computer-Assisted Drug Design

Educational Material

We have also developed some educational material on the above topics. See a short course module Geometric Methods in Structural Computational Biology which can be used under the license information specified in the same page.