February 16, Thu 2012
1:00 pm, MRB 200 Conference Room
The Center for Bioinformatics, University of Kansas
Side-chain conformational preferences upon protein-protein binding
Conformational changes in the side chains are essential for protein-protein association. Rotameric states and unbound-to-bound conformational transitions in the surface residues were systematically studied on a representative set of protein complexes. The analysis revealed characteristics of the surface side-chain conformations that can be utilized in flexible docking protocols. The number of co-crystallized complexes is much larger than the number of protein pairs with experimentally determined structures in both bound and unbound states. To increase the number of the unbound structures that can be utilized in large-scale benchmarking of docking methodologies we developed a protocol for simulating protein unbound structure from the bound one.