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Structural and Computational Biology and Molecular Biophysics

Houston, Texas

A BCM research lab.
Structural and Computational Biology & Molecular Biophysics
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Lydia Kavraki, Ph.D.

Lydia Kavraki, Ph.D.Noah Harding Professor, Computer Science

Professor, Bioengineering

Rice University

Education:

B.S. Computer Science, University of Crete, Greece, 1989
M.S. Computer Science, Stanford University, 1992
Ph.D. Computer Science, Stanford University, 1995

Research Interests:

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:

  • Bryant DH, Moll M, Finn PW and Kavraki LE. Combinatorial Clustering of Residue Position Subsets Predicts Inhibitor Affinity across the Human Kinome. PLoS Comput Biol, 9(6):e1003087 (2013). PubMed
  • Dhanik A, McMurray JS and Kavraki LE. Binding modes of peptidomimetics designed to inhibit STAT3. PLoS One, 7(12):e51603 (2012). PubMed
  • Gipson B, Hsu D, Kavraki LE and Latombe JC. Computational Models of Protein Kinematics and Dynamics: Beyond Simulation. Annu. Rev. Anal. Chem, 5:273-91 (2012). PubMed
  • Heath AP, Bennett GN and Kavraki LE. An algorithm for efficient identification of branched metabolic pathways. J. Comput. Biol. 18(11):1575-97 (2011).PubMed
  • Moll M, Bryant DH and Kavraki LE. The LabelHash algorithm for substructure matching. BMC Bioinformatics.11:555 (2010). PubMed
  • Haspel N, Moll M, Baker ML, Chiu W, and Kavraki LE. Tracing conformational changes in proteins. BMC Struct. Biol., 10:Suppl 1:S1 (2010). PubMed
  • Bryant DH, Moll M, Chen BY, Fofanov VY and Kavaraki LE. Analysis of substructural variation of enzymatic proteins with applications to protein function prediction. BMC Bioinformatics, 11:242 (2010). PubMed
  • Shehu A, Clementi C and Kavraki LE. Modeling protein conformational ensembles: from missing loops to equilibrium fluctuations. Proteins, 65(1):164-79 (2006). PubMed

For more publilcations, see listing on PubMed.

Contact Information:

Department: 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
E-mail: kavraki@rice.edu
Additional Links: Kavraki Lab, Rice University

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