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Kaushik Raha did his PhD at Penn State University in the laboratory of Prof. Kenneth M. Merz Jr. His graduate research focused on development and application of physically based computational methods to study biomolecular recognition, and led to the development of QMScore -- a quantum mechanics based energy function for scoring protein-ligand interactions. He is currently involved in algorithm development in docking at the University of California, San Francisco as a postdoctoral scholar in the laboratory of Prof. Brian Shoichet.
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Computational Studies of Protein-Ligand and Protein-Solvent Interactions
Kaushik Raha, UCSF
We have studied electrostatic properties of proteins and their interactions with solvent and ligands at various levels of theory using computational methods such as molecular dynamics simulations, molecular mechanics, and linear-scaling quantum mechanics based methods. We elucidate dielectric permittivity of proteins and find that it is a unique property that depends on the charge, composition and conformational flexibility of the protein. We have also designed a quantum mechanics based scoring function to calculate free energy of binding in protein-ligand interaction that can capture trends in diverse sets of protein-ligand complexes. We also show the importance of electrostatic interactions in discriminating native binding mode from decoy “poses”. In related studies we use pairwise decomposition of residue interaction energy to dissect the interaction between different parts of the protein and the bound ligand. Finally, we demonstrate that these methods can be used in structure based drug discovery to understand structure-activity relationships.
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