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Bioinformatics and Computational Biology Summer Institute |
Research Projects for Fellows, June 20 - August 6, 2005
P7: Predicting Protein-Protein Binding Sites Using Conservatism-of-Conservatism
| Title: | Predicting Protein-Protein Binding Sites Using Conservatism-of-Conservatism |
| Mentors: | Dr. Robert Jernigan |
| Description: | For most proteins to function, they must interact within the cellular milieu with other molecules.
Proteins interact with nucleic acids, peptides, or small molecules, but many of their interactions required for function occur
with other proteins. Although structures of many protein-protein pairs are available, this is nonetheless a small sample of all of
the possible interactions. A general methodology is needed to predict the surface regions on a protein where other proteins would be
likely to interact. Developing such computational methods is crucial to further our understanding of protein-protein interactions
essential to the selection of protein targets for rational drug-design efforts. In this project, the intern will use in-house code
to make application to a large set of protein-protein pairs to obtain predicted protein binding sites.
The intern is expected to be familiar with computational languages (FORTRAN is preferable). When there is a lack of knowledge, motivation and interest can substitute. |
| Web Resources: | |
| References: | Sen TZ, Kloczkowski A, Jernigan RL, Yan C, Honavar V, Ho KM, Wang CZ, Ihm Y, Cao H, Gu X, Dobbs D, Predicting binding sites of hydrolase-inhibitor complexes by combining several methods., BMC Bioinformatics, 5(1), 205, 2004 |