Preface ......................................................... v
Contributors ................................................... xi
Part I 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 Vqgt, and
Jürgen Bajorath
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 Holder 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 Graña-
Montes, and Salvador Ventura Zamora
15 ATTRACT and PTOOLS: Open Source Programs for Protein-
Protein Docking ............................................ 221
Sebastian Schneider, Adrien Saladin, Sébastien Fiorucci,
Chantal Prevost, and Martin Zacharias
16 Prediction of Interacting Protein Residues Using
Sequence and Structure Data ................................ 233
Vedran Franke, Mile Šikić, and Kristian Vlahoviček
Part IV Rescoring Docking Predictions
17 MM-GB/SA Rescoring of Docking Poses ........................ 255
Cristiano R.W. Guimarães
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 Guitiérrez-de-Terán and Johan Åqvist
Part V 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 Besker 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, Cesar 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
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