Human Parainfluenza Virus Project: One of the most successful projects undertaken by me is a virtual screening for inhibitors of the HPIV3 hemagglutinin-neuraminidase (HN) protein. Several inhibitors have been identified after final cell-based assays in collaboration with scientists at Weill Medical College, Cornell University, New York. This project included developing UNITY queries followed by searches, GOLD docking of hits from the UNITY search and HINT scoring of the docked positions.
Side-chain optimization algorithms using HINT: Current side-chain algorithms are successful in identifying chi1 and chi2 dihedral angles to a great extent using side-chain rotamer libraries and simple scoring functions based on probability and Van der Waal's energy. However, these scoring functions do not take into account hydrophobic interactions, H-bonds, ionic interactions and other interactions which might allow for better prediction of side-chain positions. The major aims of these projects are to write algorithms that incorporate these neglected forces and to observe if better side-chain positioning can be accomplished. If successfully implemented,
the algorithm can become a very useful tool in homology modeling. Future extensions of the program in side chain optimization during ligand docking are under consideration.
