Practical Guide to Molecular Docking

Dr. Elvis Martis is an accomplished computational chemist with over five years of experience specializing in molecular dynamics, free-energy calculations, and structure-based drug design, with a particular focus on protein-protein interactions and small-molecule discovery. His expertise spans hit identification, lead optimization, and the application of cutting-edge protein design algorithms such as Rosetta and ProteinMPNN to develop novel peptide inhibitors. With a strong foundation in pharmacy and computational chemistry, he leverages his interdisciplinary background to design innovative computational experiments that advance drug discovery efforts.He was a postdoctoral fellow at Nantes Université, where he led in-silico screening and peptide binder design projects targeting protein-protein interfaces. His prior roles include assistant professor at Bombay College of Pharmacy, where he taught organic and medicinal chemistry and supervised research projects focusing on early-phase drug discovery and molecular modeling. He is proficient in a wide range of software tools and programming languages, has contributed to multiple peer-reviewed publications, and has received several awards and fellowships recognizing his scientific achievements and research excellence.

• Introduction to Structure-based Drug Design.- Conformational Search Methods for Molecular Docking.- Scoring Functions.- Handling Biomacromolecular Structures for Molecular Docking.- Methods to Identify Binding Sites on Proteins.- Preparation of Small-Molecule Libraries.- Molecular Docking Methods and Programs.- Analysing Results from Molecular Docking.- Molecular Dynamics for Post-Processing Docking Results.- Estimating Binding Affinity by Free-Energy Methods.- Communicating Results from Molecular Docking.- FAIR and Reproducible Reporting of Molecular Docking Studies.- Union of Artificial Intelligence and Molecular Docking.- Special Topics in Molecular Docking.- In a Nutshell.