Computational Drug Discovery, 2 Volumes

Vasanthanathan Poongavanam is a senior scientist in the Department of Chemistry-BMC, Uppsala University, Sweden. Before starting at Uppsala University in 2016, he was a postdoctoral fellow at the University of Vienna, Austria, and at the University of Southern Denmark. He obtained his Ph.D. degree in Computational Medicinal Chemistry as a Drug Research Academy (DRA) Fellow at the University of Copenhagen, Denmark, on computational modeling of cytochrome P450. He has published more than 65 scientific articles, including reviews and book chapters. His scientific interests focus on in silico ADMET modeling including cell permeability and solubility, and he has worked extensively on understanding the molecular properties that govern the pharmacokinetic profile of molecules bRo5 property space, including macrocycles and PROTACs.Vijayan Ramaswamy (R.S.K. Vijayan) is a senior research scientist affiliated with the Structural Chemistry division at the Institute for Applied Cancer Science, University of Texas MD Anderson Cancer, TX, USA. In 2016, he joined MD Anderson Cancer after a brief tenure as a scientist, at PMC Advanced Technologies, New Jersey, USA. He undertook postdoctoral training at Rutgers University in New Jersey, USA, and Temple University in Pennsylvania, USA. He received his Ph.D. in Pharmacy as a CSIR senior research fellow from the Indian Institute of Chemical Biology, Kolkata, India. He is a named co-inventor on 7 issued US patents, including an ATR kinase inhibitor that has advanced to Phase 2 clinical trials. He has published more than 20 scientific articles and authored one book chapter. His research focuses on applying computational chemistry methods to drive small molecule drug discovery programs, particularly for oncology and neurodegenerative diseases.

• Volume 1Preface xvAcknowledgments xixAbout the Editors xxiPart I Molecular Dynamics and Related Methods in Drug Discovery 11 Binding Free Energy Calculations in Drug Discovery 3Anitade Ruiter and Chris Oostenbrink2 Gaussian Accelerated Molecular Dynamics in Drug Discovery 21Hung N. Do, Jinan Wang, Keya Joshi, Kushal Koirala, and Yinglong Miao3 MD Simulations for Drug-Target(Un)binding Kinetics 45Steffen Wolf4 Solvation Thermodynamics and its Applications in Drug Discovery 65Kuzhanthaivelan Saravanan and Ramesh K. Sistla5 Site-Identification by Ligand Competitive Saturation as a Paradigm of Co-solvent MD Methods 83Asuka A. Orr and Alexander D. MacKerell Jr.Part II Quantum Mechanics Application for Drug Discovery 1196 QM/MM for Structure-Based Drug Design: Techniques and Applications 121Marc W. van der Kamp and Jaida Begum7 Recent Advances in Practical Quantum Mechanics and Mixed-QM/MM-Driven X-Ray Crystallography and Cryogenic Electron Microscopy (Cryo-EM) and Their Impact on Structure-Based Drug Discovery 157Oleg Borbulevych and Lance M. Westerhoff8 Quantum-Chemical Analyses of Interactions for Biochemical Applications 183Dmitri G. FedorovPart III Artificial Intelligence in Pre-clinical Drug Discovery 2119 The Role of Computer-Aided Drug Design in Drug Discovery 213Stormvander Voort, Andreas Bender, and Bart A. Westerman10 AI-Based Protein Structure Predictions and Their Implications in Drug Discovery 227Tahsin F. Kellici, Dimitar Hristozov, and Inaki Morao11 Deep Learning for the Structure-Based Binding Free Energy Prediction of Small Molecule Ligands 255Venkatesh Mysore, Nilkanth Patel, and Adegoke Ojewole12 Using Artificial Intelligence for de novo Drug Design and Retrosynthesis 275Rohit Arora, Nicolas Brosse, Clarisse Descamps, Nicolas Devaux, Nicolas Do Huu, Philippe Gendreau, Yann Gaston-Mathé, Maud Parrot, Quentin Perron, and Hamza Tajmouati13 Reliability and Applicability Assessment for Machine Learning Models 299Fabio Urbina and Sean EkinsVolume 2Preface xvAcknowledgments xixAbout the Editors xxiPart IV Chemical Space and Knowledge-Based Drug Discovery 31514 Enumerable Libraries and Accessible Chemical Space in Drug Discovery 317Tim Knehans, Nicholas A. Boyles, and Pieter H. Bos15 Navigating Chemical Space 337Akos Tarcsay, András Volford, Jonathan Buttrick, Jan-Constantin Christopherson, Máte Erdos, and Zoltán B. Szabó16 Visualization, Exploration, and Screening of Chemical Space in Drug Discovery 365José J. Naveja, Fernanda I. Saldívar-González, Diana L. Prado-Romero, Angel J.Ruiz-Moreno, Marco Velasco-Velázquez, Ramón Alain Miranda-Quintana, and José L. Medina-Franco17 SAR Knowledge Bases for Driving Drug Discovery 395Nishanth Kandepedu, Anil Kumar Manchala, and Norman Azoulay18 Cambridge Structural Database (CSD)–Drug Discovery Through Data Mining & Knowledge-Based Tools 419Francesca Stanzione, Rupesh Chikhale, and Laura FriggeriPart V Structure-Based Virtual Screening Using Docking 44119 Structure-Based Ultra-Large Virtual Screenings 443Christoph Gorgulla20 Community Benchmarking Exercises for Docking and Scoring 471Bharti Devi, Anurag TK Baidya, and Rajnish KumarPartVI In Silico ADMET Modeling 49521 Advances in the Application of In Silico ADMET Models–An Industry Perspective 497Wenyi Wang, Fjodor Melnikov, Joe Napoli, and Prashant DesaiPart VII Computational Approaches for New Therapeutic Modalities 53722 Modeling the Structures of Ternary Complexes Mediated by Molecular Glues 539Michael L. Drummond23 Free Energy Calculations in Covalent Drug Design 561Levente M. Mihalovits, György G. Ferenczy, and György M. KeseruPart VIII Computing Technologies Driving Drug Discovery 57924 Orion A Cloud-Native Molecular Design Platform 581Jesper Sorensen, Caitlin C. Bannan, Gaetano Calabrò, Varsha Jain, Grigory Ovanesyan, Addison Smith, She Zhang, Christopher I. Bayly, Tom A. Darden, Matthew T. Geballe, David N. LeBard, Mark McGann, Joseph B. Moon, Hari S. Muddana, Andrew Shewmaker, Jharrod LaFon, Robert W. Tolbert, A. Geoffrey Skillman, and Anthony Nicholls25 Cloud-Native Rendering Platform and GPUs Aid Drug Discovery 617Mark Ross, Michael Drummond, Lance Westerhoff, Xavier Barbeu, Essam Metwally, Sasha Banks-Louie, Kevin Jorissen, Anup Ojah, and Ruzhu Chen26 The Quantum Computing Paradigm 627Thomas Ehmer, Gopal Karemore, and Hans MeloIndex 679