Produktbild: Computational Drug Discovery
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Computational Drug Discovery Methods and Applications

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Beschreibung

Produktdetails

Einband

Gebundene Ausgabe

Erscheinungsdatum

21.02.2024

Herausgeber

Vasanthanathan Poongavanam + weitere

Verlag

Wiley-VCH

Seitenzahl

736

Maße (L/B/H)

25,1/17,6/4,4 cm

Gewicht

1688 g

Auflage

1. Auflage

Sprache

Englisch

ISBN

978-3-527-35166-4

Beschreibung

Portrait

Vasanthanathan Poongavanam is a senior researcher in the Department of Chemistry-BMC, Uppsala University, Sweden. Before starting at Uppsala University in a researcher position with Jan Kihlberg 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. in medicinal chemistry as

a Drug Research Academy Fellow at the University of Copenhagen, Denmark, on computational modeling of Cytochrome P450. His research interests focus on understanding the molecular properties that govern the pharmacokinetic profile of molecules beyond the Ro5 space, including macrocycles and PROTACs.

Vijayan Ramaswamy is a research scientist with the Structural Chemistry group at the Institute for Applied Cancer Science, University of Texas MD Anderson Cancer, TX, USA. Before starting at the MD Anderson Cancer in 2016, he was a postdoctoral fellow at Rutgers University, NJ, USA, and at Temple University, PA, USA. He received his Ph.D as a CSIR senior research fellow from the Indian Institute of Chemical Biology, Kolkata, India. His research focuses on applying computational chemistry methods to drive small-molecule drug discovery programs, particularly in oncology and neurodegenerative diseases.

Produktdetails

Einband

Gebundene Ausgabe

Erscheinungsdatum

21.02.2024

Herausgeber

Verlag

Wiley-VCH

Seitenzahl

736

Maße (L/B/H)

25,1/17,6/4,4 cm

Gewicht

1688 g

Auflage

1. Auflage

Sprache

Englisch

ISBN

978-3-527-35166-4

Herstelleradresse

Wiley-VCH GmbH
Boschstraße 12
69469 Weinheim
DE

Email: [email protected]

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  • Produktbild: Computational Drug Discovery
  • 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-Mathé, 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, András Volford, Jonathan Buttrick, Jan-Constantin Christopherson, Máte Erdos, and Zoltán B. Szabó

    16 Visualization, Exploration, and Screening of Chemical Space in Drug Discovery 365
    José 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-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, György G. Ferenczy, and György 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 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 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