Computational Drug Discovery, 2 Volumes

Volume 1

Preface xv

Acknowledgments xix

About the Editors xxi

Part I Molecular Dynamics and Related Methods in Drug Discovery 1

1 Binding Free Energy Calculations in Drug Discovery 3
Anitade Ruiter and Chris Oostenbrink

2 Gaussian Accelerated Molecular Dynamics in Drug Discovery 21
Hung N. Do, Jinan Wang, Keya Joshi, Kushal Koirala, and Yinglong Miao

3 MD Simulations for Drug-Target(Un)binding Kinetics 45
Steffen Wolf

4 Solvation Thermodynamics and its Applications in Drug Discovery 65
Kuzhanthaivelan Saravanan and Ramesh K. Sistla

5 Site-Identification by Ligand Competitive Saturation as a Paradigm of Co-solvent MD Methods 83
Asuka A. Orr and Alexander D. MacKerell Jr.

Part II Quantum Mechanics Application for Drug Discovery 119

6 QM/MM for Structure-Based Drug Design: Techniques and Applications 121
Marc W. van der Kamp and Jaida Begum

7 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 157
Oleg Borbulevych and Lance M. Westerhoff

8 Quantum-Chemical Analyses of Interactions for Biochemical Applications 183
Dmitri G. Fedorov

Part III Artificial Intelligence in Pre-clinical Drug Discovery 211

9 The Role of Computer-Aided Drug Design in Drug Discovery 213
Stormvander Voort, Andreas Bender, and Bart A. Westerman

10 AI-Based Protein Structure Predictions and Their Implications in Drug Discovery 227
Tahsin F. Kellici, Dimitar Hristozov, and Inaki Morao

11 Deep Learning for the Structure-Based Binding Free Energy Prediction of Small Molecule Ligands 255
Venkatesh Mysore, Nilkanth Patel, and Adegoke Ojewole

12 Using Artificial Intelligence for de novo Drug Design and Retrosynthesis 275
Rohit Arora, Nicolas Brosse, Clarisse Descamps, Nicolas Devaux, Nicolas Do Huu, Philippe Gendreau, Yann Gaston-Mathe, Maud Parrot, Quentin Perron, and Hamza Tajmouati

13 Reliability and Applicability Assessment for Machine Learning Models 299
Fabio Urbina and Sean Ekins

Volume 2

Preface xv

Acknowledgments xix

About the Editors xxi

Part IV Chemical Space and Knowledge-Based Drug Discovery 315

14 Enumerable Libraries and Accessible Chemical Space in Drug Discovery 317
Tim Knehans, Nicholas A. Boyles, and Pieter H. Bos

15 Navigating Chemical Space 337
Akos Tarcsay, Andras Volford, Jonathan Buttrick, Jan-Constantin Christopherson, Mate Erdos, and Zoltan B. Szabo

16 Visualization, Exploration, and Screening of Chemical Space in Drug Discovery 365
Jose J. Naveja, Fernanda I. Saldivar-Gonzalez, Diana L. Prado-Romero, Angel J.Ruiz-Moreno, Marco Velasco-Velazquez, Ramon Alain Miranda-Quintana, and Jose L. Medina-Franco

17 SAR Knowledge Bases for Driving Drug Discovery 395
Nishanth Kandepedu, Anil Kumar Manchala, and Norman Azoulay

18 Cambridge Structural Database (CSD)-Drug Discovery Through Data Mining & Knowledge-Based Tools 419
Francesca Stanzione, Rupesh Chikhale, and Laura Friggeri

Part V Structure-Based Virtual Screening Using Docking 441

19 Structure-Based Ultra-Large Virtual Screenings 443
Christoph Gorgulla

20 Community Benchmarking Exercises for Docking and Scoring 471
Bharti Devi, Anurag TK Baidya, and Rajnish Kumar

PartVI In Silico ADMET Modeling 495

21 Advances in the Application of In Silico ADMET Models-An Industry Perspective 497
Wenyi Wang, Fjodor Melnikov, Joe Napoli, and Prashant Desai

Part VII Computational Approaches for New Therapeutic Modalities 537

22 Modeling the Structures of Ternary Complexes Mediated by Molecular Glues 539
Michael L. Drummond

23 Free Energy Calculations in Covalent Drug Design 561
Levente M. Mihalovits, Gyoergy G. Ferenczy, and Gyoergy M. Keseru

Part VIII Computing Technologies Driving Drug Discovery 579

24 Orion A Cloud-Native Molecular Design Platform 581
Jesper Sorensen, Caitlin C. Bannan, Gaetano Calabro, 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 Nicholls

25 Cloud-Native Rendering Platform and GPUs Aid Drug Discovery 617
Mark Ross, Michael Drummond, Lance Westerhoff, Xavier Barbeu, Essam Metwally, Sasha Banks-Louie, Kevin Jorissen, Anup Ojah, and Ruzhu Chen

26 The Quantum Computing Paradigm 627
Thomas Ehmer, Gopal Karemore, and Hans Melo

Index 679

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• Farmacologia
• Tecnologia farmacêutica
• Tecnologia da informação: aspectos gerais
• Fabricação auxiliada por computador

Protein structure prediction: ligand based virtual screening; structure based virtual screening; multi-parameter optimization; generative chemistry; computer-aided synthesis planning; Quantum computing; ADMET