[转移贴]Computational Drug Discovery and Design

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原贴由wwwkkk83发表于 2012-1-9 14:39  可惜下载连接已失效，欢迎有原书的补充下载链接，多谢。

Book Description
Hardcover: 645 pages
Publisher: Humana Press; 2012 edition (December 21, 2011)
Language: English
ISBN-10: 1617794643
ISBN-13: 978-1617794643


Due to the rapid and steady growth of available low-cost computer power, the use of computers for discovering and designing new drugs is becoming a central topic in modern molecular biology and medicinal chemistry. In Computational Drug Discovery and Design: Methods and Protocols expert researchers in the field provide key techniques to investigate biomedical applications for drug developments based on computational chemistry. These include methods and techniques from binding sites prediction to the accurate inclusion of solvent and entropic effects, from high-throughput screening of large compound databases to the expanding area of protein-protein inhibition, toward quantitative free-energy approaches in ensemble-based drug design using distributed computing. Written in the highly successful Methods in Molecular Biology™ series format, chapters include introductions to their respective topics, reference to software and open source analysis tools, step-by-step, readily reproducible computational protocols, and key tips on troubleshooting and avoiding known pitfalls.   Thorough and intuitive, Computational Drug Discovery and Design: Methods and Protocols aids scientists in the continuing study of state-of-the-art concepts and computer-based methodologies.

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Contents

Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v

Contributors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xi


PARTI DRUG BINDING SITE PREDICTION, DESIGN, AND DESCRIPTORS

1 A Molecular Dynamics Ensemble-Based Approach for the Mapping
of Druggable Binding Sites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Anthony Ivetac and J. Andrew McCammon

2 Analysis of Protein Binding Sites by Computational Solvent Mapping . . . . . . . . . . . 13
David R. Hall, Dima Kozakov, and Sandor Vajda

3 Evolutionary Trace for Prediction and Redesign of Protein Functional Sites . . . . . . 29
Angela Wilkins, Serkan Erdin, Rhonald Lua, and Olivier Lichtarge

4 Information Entropic Functions for Molecular Descriptor Profiling . . . . . . . . . . . . . 43
Anne Mai Wassermann, Britta Nisius, Martin Vogt,
and J PART II VIRTUAL SCREENING OF LARGE COMPOUND LIBRARIES:
INCLUDING MOLECULAR FLEXIBILITY

5 Expanding the Conformational Selection Paradigm
in Protein-Ligand Docking . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Guray Kuzu, Ozlem Keskin, Attila Gursoy, and Ruth Nussinov

6 Flexibility Analysis of Biomacromolecules with Application
to Computer-Aided Drug Design . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Simone Fulle and Holger Gohlke

7 On the Use of Molecular Dynamics Receptor Conformations
for Virtual Screening. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
Sara E. Nichols, Riccardo Baron, and J. Andrew McCammon

8 Virtual Ligand Screening Against Comparative Protein Structure Models . . . . . . . . 105
Hao Fan, John J. Irwin, and Andrej Sali

9 AMMOS Software: Method and Application. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
Tania Pencheva, David Lagorce, Ilza Pajeva, Bruno O. Villoutreix,
and Maria A. Miteva

10 Rosetta Ligand Docking with Flexible XML Protocols . . . . . . . . . . . . . . . . . . . . . . . . 143
Gordon Lemmon and Jens Meiler

11 Normal Mode-Based Approaches in Receptor Ensemble Docking. . . . . . . . . . . . . . . 157
Claudio N. Cavasotto

12 Application of Conformational Clustering in Protein–Ligand Docking. . . . . . . . . . . 169
Giovanni Bottegoni, Walter Rocchia, and Andrea Cavalli

13 How to Benchmark Methods for Structure-Based Virtual Screening
of Large Compound Libraries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187
Andrew J. Christofferson and Niu Huang
PART III PREDICTION OF PROTEIN-PROTEIN DOCKING AND INTERACTIONS

14 AGGRESCAN: Method, Application, and Perspectives for Drug Design . . . . . . . . . 199
Natalia S. de Groot, Virginia Castillo, Ricardo Gran˜a-Montes,
and Salvador Ventura Zamora

15 ATTRACT and PTOOLS: Open Source Programs
for Protein–Protein Docking . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 221
Sebastian Schneider, Adrien Saladin, Se′bastien Fiorucci,
Chantal Pre′vost, and Martin Zacharias

16 Prediction of Interacting Protein Residues
Using Sequence and Structure Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 233
Vedran Franke, Mile S ˇ ikic′, and Kristian Vlahovicˇek


PART IV RESCORING DOCKING PREDICTIONS

17 MM-GB/SA Rescoring of Docking Poses. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255
Cristiano R.W. Guimara˜es

18 A Case Study of Scoring and Rescoring in Peptide Docking. . . . . . . . . . . . . . . . . . . . 269
Zunnan Huang and Chung F. Wong

19 The Solvated Interaction Energy Method for Scoring Binding Affinities . . . . . . . . . 295
Traian Sulea and Enrico O. Purisima

20 Linear Interaction Energy: Method and Applications in Drug Design . . . . . . . . . . . 305
Hugo Guitie′rrez-de-Tera′n and Johan A ° qvist

PARTV CRUCIAL NEGLECTED EFFECTS: ENTROPY,
SOLVENT, AND PROTONATION

21 Estimation of Conformational Entropy in Protein–Ligand Interactions:
A Computational Perspective . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 327
Anton A. Polyansky, Ruben Zubac, and Bojan Zagrovic

22 Explicit Treatment of Water Molecules in Data-Driven Protein–Protein
Docking: The Solvated HADDOCKing Approach. . . . . . . . . . . . . . . . . . . . . . . . . . . . 355
Panagiotis L. Kastritis, Aalt D.J. van Dijk, and Alexandre M.J.J. Bonvin

23 Protein–Water Interactions in MD Simulations: POPS/POPSCOMP Solvent
Accessibility Analysis, Solvation Forces and Hydration Sites . . . . . . . . . . . . . . . . . . . . 375
Arianna Fornili, Flavia Autore, Nesrine Chakroun,
Pierre Martinez, and Franca Fraternali

24 Computing the Thermodynamic Contributions of Interfacial Water . . . . . . . . . . . . . 393
Zheng Li and Themis Lazaridis

25 Assignment of Protonation States in Proteins and Ligands:
Combining pKa Prediction with Hydrogen Bonding Network Optimization. . . . . . 405
Elmar Krieger, Roland Dunbrack, Rob Hooft,
and Barbara Krieger


PART VI TOWARD THE USE OF ROBUST FREE ENERGY
METHODS IN DRUG DESIGN

26 Best Practices in Free Energy Calculations for Drug Design . . . . . . . . . . . . . . . . . . . . 425
Michael R. Shirts

27 Independent-Trajectory Thermodynamic Integration: A Practical
Guide to Protein-Drug Binding Free Energy Calculations
Using Distributed Computing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 469
Morgan Lawrenz, Riccardo Baron, Yi Wang, and J. Andrew McCammon

28 Free Energy Calculations from One-Step Perturbations . . . . . . . . . . . . . . . . . . . . . . . 487
Chris Oostenbrink

29 Using Metadynamics and Path Collective Variables to Study Ligand
Binding and Induced Conformational Transitions . . . . . . . . . . . . . . . . . . . . . . . . . . . . 501
Neva Besˇker and Francesco L. Gervasio

30 Accelerated Molecular Dynamics in Computational Drug Design . . . . . . . . . . . . . . . 515
Jeff Wereszczynski and J. Andrew McCammon
PART VII BIOMEDICAL APPLICATIONS

31 Molecular Dynamics Applied in Drug Discovery:
The Case of HIV-1 Protease . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 527
Yi Shang and Carlos Simmerling

32 Decomposing the Energetic Impact of Drug-Resistant Mutations:
The Example of HIV-1 Protease–DRV Binding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 551
Yufeng Cai and Celia Schiffer

33 Guide to Virtual Screening: Application to the Akt Phosphatase PHLPP . . . . . . . . . 561
William Sinko, Emma Sierecki, Ce′sar A.F. de Oliveira,
and J. Andrew McCammon

34 Molecular-Level Simulation of Pandemic Influenza Glycoproteins . . . . . . . . . . . . . . 575
Rommie E. Amaro and Wilfred W. Li

35 Homology Modeling of Cannabinoid Receptors: Discovery
of Cannabinoid Analogues for Therapeutic Use . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 595
Chia‐en A. Chang, Rizi Ai, Michael Gutierrez, and Michael J. Marsella

36 High-Throughput Virtual Screening Lead to Discovery of Non-Peptidic
Inhibitors of West Nile Virus NS3 Protease. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 615
Danzhi Huang

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 625