Tropsha Awarded NSF Grant to Design Tools to Analyze Protein-Protein Interactions
The interactions between proteins play a central role in all major signaling events that occur in living cells. However, many if not most pairs of interacting proteins remain unknown, and their discovery presents a key challenge for postgenomic biology, says Tropsha, the K.H. Lee Distinguished Professor in the School’s Division of Chemical Biology and Medicinal Chemistry.
“We plan to create and deliver—ultimately in the form of user-friendly software—novel approaches to analyzing protein-protein interactions that employ a unique combination of concepts at the interface of structural bioinformatics, computational geometry, and cheminformatics,” Tropsha says.
The researchers are developing a new family of cheminformatics descriptors of PPIs derived from Delaunay tessellation of PPI interface that they are calling SNAP3 (Simplicial Neighborhood Analysis of Protein-Protein Packing) that are based on the SNAPP approach developed earlier by the group. They will employ the SNAP3 descriptors to develop both analytical and QSAR-like scoring functions that will be employed both for hot-spot identification and protein (peptide) docking. These descriptors are used to identify hot-spot regions on protein surfaces and predict the structure of protein-protein (or protein-peptide) complexes using a new GridDock docking method to be developed in this project.
The web portal for the project can be found at http://chembench.mml.unc.edu/PPI.
Coprincipal investigators on the grant are Denis Fourches, PhD, associate director of the Laboratory for Molecular Modeling, and Diane Pozefsky, PhD, a research professor in the UNC Department of Computer Science.