Lipari School on BioInformatics and Computational Biology
Jacob T. Schwartz International School for Scientific ResearchLydia Kavraki, Rice, Houston, Texas, USA
Geometry and robotics-inspired methods for the analysis of protein function and the design of new medicines
The design of better and tailor-made medicines through pharacogenomics analysis
involves, among others, the detailed study of protein structure, flexibility, and
function. The lectures in this course will describe recent computational techniques
that can complement and guide experimentation for understanding molecular
interactions. The topics that will be covered include: computational issues in
modeling molecules, the characterization of the flexibility of small proteins using
a robotics-inspired approach, the analysis of the conformational space of large
complexes, and data-driven analysis for understanding how structural variability
within a family of functionally-related proteins fine-tunes their function.
Relevant material:
- http://cnx.org/content/col10344/latest/
- Shehu A, Kavraki LE. Modeling structures and motions of loops in protein molecules. Submitted. (Available by March 2012).
- Haspel, N, Moll M, Baker ML, Chiu W, Kavraki LE. 2010. Tracing conformational changes in proteins. BMC Structural Biology. 10:S1.
- Moll, M, Bryant DH, Kavraki LE. 2010. The LabelHash algorithm for substructure matching. BMC Bioinformatics. 11(1):555.
- Bryant, DH, Moll M, Chen BY, Fofanov VY, Kavraki LE. 2010. Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction. BMC Bioinformatics. 11:242.
- Shehu, A, Kavraki LE, Clementi C. 2009. Multiscale characterization of protein conformational ensembles. Proteins. 76:837-851.