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Lydia E. Kavraki
Rice UniversityDepartment: Computer Science, Rice University ; Bioengineering, Rice University (Joint Appointment)Address: Computer Science MS132 3106 Duncan Hall 6100 S. Main St. Houston, TX 77005-1892 Phone: 713-348-5737 Fax: 713-348-5930 Email: kavraki@rice.edu Web: www.cs.rice.edu/~kavraki |
Education
B.S. Computer Science, University of Crete, Greece, 1989
M.S. Computer Science, Stanford University, 1992
Ph.D. Computer Science, Stanford University, 1995
Honors
Fellow, AIMBE.
Fellow, WTN.
Duncan Award for Excellence in Research and Teaching, Rice University.
Top 100 Young Innovators by MIT's Technology Review Magazine.
Brilliant 10, Popular Science Magazine
Early Career Award of the IEEE Robotics and Automation Society.
ACM Grace Murray Hopper Award.
Sloan Fellowship.
Research Topic
Computation of Shape and Motion in Biology, Computer-Assisted Drug Design
Research Description
In Bioinformatics Kavraki's group develops 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, and the understanding and compact representation of structural changes in large biomolecular machines. We apply robotics, computational geometry, and probabilistic analysis methods to the above problems.
Lydia Kavraki is an associate editor of the IEEE/ACM Transactions on Computational Biology and Bioinformatics and the Computer Science Reviews.
Selected Publications
- Teodoro, M.L., Phillips, G.N., Jr. and Kavraki, L.E. (2003). Understanding protein flexibility through dimensionality reduction. J. Comput. Biol. 10: 617-634.
- Teodoro, M.L. and Kavraki, L.E. (2003). Conformational flexibility models for the receptor in structure based drug design. Curr. Pharm. Design 9: 1419-1431.
- Zhang, M. and Kavraki, L.E. (2002). A new method for fast and accurate derivation of molecular conformations. J. Chem. Inf. Comput. Sci. 42: 64-70.
- H. Yao, D. Kristensen, I. Mihalek, M. Sowa, Ch. Shaw, M. Kimmel, L.E. Kavraki, and O. Lichtarge (2003). An Accurate, Scalable Method to Identify Functional Sites in Protein Structures, Journal of Molecular Biology, 326(1), 255-261.
- M. Teodoro, G.N. Phillips, Jr., and L.E. Kavraki. (2001). Molecular Docking: A Problem with Thousands of Degrees of Freedom. IEEE International Conference on Robotics and Automation, Seoul, Korea.
- S.M. LaValle, P.W. Finn, L.E. Kavraki, and J.C. Latombe. (2000). A Randomized Kinematics-based Approach to Pharmacophore-Constrained Conformational Search and Database Screening. J. Comput. Chem. 21:731-747.
- M. Zhang, R.A. White, L. Wang, R. Goldman, L.E. Kavraki and B. Hassett. Improving Conformational Searches by Geometric Screening. Bioinformatics, 21(5), 2005, 624 - 630.
Lab Members
Current Graduate Students
Former Grad Students
Current Post Docs
Former Post Docs
Lab Photos
Last edited on: September 21, 2009