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E-raamat: In Silico Drug Discovery and Design: Theory, Methods, Challenges, and Applications

  • Formaat: 558 pages
  • Ilmumisaeg: 06-Aug-2015
  • Kirjastus: CRC Press Inc
  • Keel: eng
  • ISBN-13: 9781482217858
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  • Formaat: 558 pages
  • Ilmumisaeg: 06-Aug-2015
  • Kirjastus: CRC Press Inc
  • Keel: eng
  • ISBN-13: 9781482217858

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In Silico Drug Discovery and Design: Theory, Methods, Challenges, and Applications provides a comprehensive, unified, and in-depth overview of the current methodological strategies in computer-aided drug discovery and design. Its main aims are to introduce the theoretical framework and algorithms, discuss the range of validity, strengths and limitations of each methodology, and present applications to real world problems in the drug discovery arena. Special emphasis has been given to the emerging and most pressing methodological challenges in in silico drug discovery and design.The book assumes a basic knowledge of physical principles and molecular modeling. Particular attention has been paid to outline the underlying physico-chemical foundation of the methods described, thus providing the necessary background to avoid a "black-box" approach. In each self-contained chapter, this is presented together with the latest developments and applications, and the challenges that lie ahead.Assembling a unique team of experts to weigh in on the most important issues influencing modern computational drug discovery and design, this book constitutes both a desktop reference to academic and industrial researchers in the field, and a textbook for students in the area of molecular modeling and drug discovery.Comprised of 18 chapters and divided into three parts, this book: Provides a comprehensive, unified, and in-depth overview of the current methodological strategies in computer-aided drug discovery and designOutlines the underlying physico-chemical foundation of the methods describedPresents several applications of computational methods to real world problems in the drug design fieldHelps to avoid a "black-box" approach to in silico drug discoveryConstitutes an actual textbook for students in the area of molecular modeling and drug discoveryGives the reader the adequate background to face the current challenges of the fieldIn Silico Drug Discovery and Design: Theory, Methods, Challenges, and Applications describes the theoretical framework, methods, practical applications and case examples relevant to computer-aided drug lead discovery and design. This text will surely aid in understanding the underlying physical foundation of computational tools and their range of application, thus facilitating the interpretation of simulation results.

Arvustused

"... an ambitious book which delivers a great deal of material in one volume. ... a useful addition to the small number of accessible and authoritative books on the subject." ChemMedChem, 2016, 11, 638

" With this book the lids on the algorithm black boxes are lifted and all within the field can clearly see their inner workings. This book also has the capacity to enthusiastically galvanize those at the cutting-edge of algorithm development. The Thorny problems remaining are illuminated and attacked with vigor, such as how target flexibility and solvation at molecular interfaces can be more accurately modeled and how this may ultimately feed into a better determination of BINDING free energies and the calculation of accurate kinetic parameters." Dr. Paul A Bates, The Francis Crick Institute

" a solid, current, well-written and well-organized set of reviews of important topics in in silico drug discovery. It should be useful for readers, ranging from students to senior scientists, who are looking for accessible overviews of this material." Mike Gilson, University of California, San Diego, USA

Preface vii
Editor xi
Contributors xiii
Section I Theory, Methods, and Applications
1 The Physical Basis of Ligand Binding
3(42)
Thomas Simonson
2 Force-Field Representation of Biomolecular Systems
45(34)
Meagan C. Small
Alexander D. MacKerell, Jr.
3 Library Design, Chemical Space, and Drug Likeness
79(20)
Hugo O. Villar
4 Ligand-Based Drug Discovery and Design
99(24)
Alvaro Cortes-Cabrera
Pedro A. Sanchez Murcia
Antonio Morreale
Federico Gago
5 Pharmacophore Modeling and Pharmacophore-Based Virtual Screening
123(32)
Muhammad Akram
Teresa Kaserer
Daniela Schuster
6 Protein--Ligand Docking: From Basic Principles to Advanced Applications
155(34)
Christoph A. Sotriffer
7 Protein--Ligand Docking: Virtual Screening and Applications to Drug Discovery
189(26)
Antonella Ciancetta
Stefano Moro
8 Protein Structure Modeling in Drug Design
215(34)
Damian Palomba
Claudio N. Cavasotto
9 Implicit Solvation Methods in the Study of Ligand--Protein Interactions
249(28)
William Zamora
Josep M. Campanera
F. Javier Luque
Section II Advanced Techniques
10 Toward Complete Cellular Pocketomes and Predictive Polypharmacology
277(16)
Ruben A. Abagyan
Bryn Taylor
11 MM-GB/SA Rescoring of Docking Poses: Tricks of the Trade
293(20)
Cristiano R. W. Guimaraes
12 Free Energy Calculations of Ligand--Protein Binding
313(24)
Rainer Bomblies
Manuel Luitz
Martin Zacharias
13 Molecular Mechanics/Coarse-Grained Simulations as a Structural Prediction Tool for GPCRs/Ligand Complexes
337(16)
Francesco Musiani
Alejandro Giorgetti
Paolo Carloni
14 Fragment-Based Methods in Drug Design
353(40)
Marton Vass
Gergely Makara
Gyorgy Miklos Keseru
Section III Challenges
15 Role of Water Molecules and Hydration Properties in Modeling Ligand--Protein Interaction and Drug Design
393(18)
Alfonso T. Garcia-Sosa
16 How Protein Flexibility Can Influence Docking/Scoring Simulations
411(30)
Pietro Cozzini
Luca Dellafiora
Tiziana Ginex
Francesca Spyrakis
17 In Silico Approaches Assisting the Rational Design of Low Molecular Weight Protein--Protein Interaction Modulators
441(42)
Bruno O. Villoutreix
Melaine A. Kuenemann
David Lagorce
Olivier Sperandio
Maria A. Miteva
18 Incorporating Binding Kinetics in Drug Design
483(22)
Chung F. Wong
Index 505
Claudio N. Cavasotto earned his MSc and PhD in physics from the University of Buenos Aires. He conducted his postdoctoral training at The Scripps Research Institute after which in 2002 he moved to MolSoft LLC, La Jolla, California, as senior research scientist, where he remained until 2007. He then became assistant and associate professor at the School of Biomedical Informatics at the University of Texas Health Science Center at Houston. In 2012 he moved to the Biomedicine Research Institute of Buenos Aires-Partner Institute of the Max Planck Society, where he is head of Computational Chemistry and Drug Design. His research interests are primarily biomolecular simulation, computer-aided drug discovery and cheminformatics. His group develops and applies computational methods to study molecular interactions in biological systems, and to design molecules which modulate targets of pharmaceutical relevance.