<i>Sanjeevini: </i>A comprehensive active site directed lead design software

Abstract

<i>Sanjeevini</i> - a comprehensive active site directed lead compound design software, based on the on-going research in our laboratory, is described here. The computational pathway integrates several protocols proceeding from the design of chemical templates to lead-like molecules, given the three dimensional structure of the target protein and a definition of its

active site. A conscious attempt has been made to handle the target biomolecule and the candidate drug molecules at the atomic level retaining system independence while providing access for systematic improvements at the force field level. Concerns related to geometry of the molecules, partial atomic charges, docking of candidates in the active site, flexibility

and solvent effects are accounted for at the current state-of-the-art. To ensure theoretical ri gor, binding free energy estimates are developed for candidate molecules with the target protein within the framework of statistical mechanics. We present herein, the technical and scientific features of <i>Sanjeevini, </i>its validation and scope for further improvement. Some modules of <i>Sanjeevini </i>have been made accessible at http ://www.scfbio-iitd.res. in/drugdes/ sanjeevini.html.