In recent years we have seen a rise in the use of 
computer-aided drug design tools in pharmaceutical companies as a result of advances in the underlying methods coupled with vast increases in computational resources. Here, we present an overview of the tools in the Schrödinger Suites, including ligand-based and structure-based approaches. We show that improvements in the underlying force field can improve results across a broad range of applications. We also show that molecular dynamics simulations can be used to accurately predict protein conformational states and protein-ligand binding free energies. Woody Sherman is Vice President of Applications Science at Schrödinger. He received his B.S. in Physical Chemistry from the University of California at Santa Barbara where he studied nonlinear optical properties of organic polymers using computational quantum mechanics. He completed his Ph.D. at MIT working in Professor Bruce Tidor’s lab where he examined the role of electrostatics in protein-ligand binding and implemented a novel method for optimizing ligand binding specificity across a panel of targets. While in graduate school he completed an internship at Biogen where he helped develop novel methods to enhance antibody affinity through electrostatic charge optimization, resulting in a publication and patent. At Schrödinger, he is involved in applications projects, product development, methods development, and scientific software support. He also works closely with customers on research projects and collaborations. Woody has published on a broad range of topics, including induced-fit docking, ensemble docking, protein design, small molecule optimization, cheminformatics, hybrid ligand/structure-based methods, free energy simulations, charge optimization, pharmacophore modeling, and more. He is a reviewer for top journals in computational chemistry and drug design and is on the Editorial Board of both Chemical Biology & Drug Design and Journal of Chemical Information and Modeling.
