A molecular dynamics ensemble-based approach for the mapping of druggable binding sites / Anthony Ivetac and J. Andrew McCammon -- Analysis of protein binding sites by computational solvent mapping / David R. Hall, Dima Kozakov, and Sandor Vajda -- Evolutionary trace for prediction and redesign of protein functional sites / Angela Wilkins [and others] -- Information entropic functions for molecular descriptor profiling / Anne Mai Wassermann [and others] -- Expanding the conformational selection paradigm in protein-ligand docking / Guray Kuzu [and others] -- Flexibility analysis of biomacromolecules with application to computer-aided drug design / Simone Fulle and Holger Gohlke -- On the use of molecular dynamics receptor conformations for virtual screening / Sara E. Nichols, Riccardo Baron, and J. Andrew McCammon -- Virtual ligand screening against comparative protein structure models / Hao Fan, John J. Irwin, and Andrej Sali -- AMMOS software : method and application / Tania Pencheva [and others] -- Rosetta ligand docking with flexible XML protocols / Gordon Lemmon and Jens Meiler -- Normal mode-based approaches in receptor ensemble docking / Claudio N. Cavasotto -- Application of conformational clustering in protein-ligand docking / Giovanni Bottegoni, Walter Rocchia, and Andrea Cavalli -- How to benchmark methods for structure-based virtual screening of large compound libraries / Andrew J. Christofferson and Niu Huang -- AGGRESCAN : method, application, and perspectives for drug design / Natalia S. de Groot [and others] -- ATTRACT and PTOOLS : open source programs for protein-protein docking Sebastian Schneider [and others] -- Prediction of interacting protein residues using sequence and structure data / Vedran Franke, Mile Šikić, and Kristian Vlahoviček -- MM-GB/SA rescoring of docking poses / Cristiano R.W. Guimarães -- A case study of scoring and rescoring in peptide docking / Zunnan Huang and Chung F. Wong -- The solvated interaction energy method for scoring binding affinities / Traian Sulea and Enrico O. Purisima -- Linear interaction energy : method and applications in drug design / Hugo Guitiérrez-de-Terán and Johan Åqvist -- Estimation of conformational entropy in protein-ligand interactions : a computational perspective / Anton A. Polyansky, Ruben Zubac, and Bojan Zagrovic -- Explicit treatment of water molecules in data-driven protein-protein docking : the solvated HADDOCKing approach / Panagiotis L. Kastritis, Aalt D.J. van Dijk, and Alexandre M.J.J. Bonvin -- Protein-water interactions in MD simulations : POPS/POPSCOMP solvent accessibility analysis, solvation forces and hydration sites / Arianna Fornili [and others] -- Computing the thermodynamic contributions of interfacial water / Zheng Li and Themis Lazaridis -- Assignment of protonation states in proteins and ligands : combining pKa prediction with hydrogen bonding network optimization / Elmar Krieger [and others] -- Best practices in free energy calculations for drug design / Michael R. Shirts -- Independent-trajectory thermodynamic integration : a practical guide to protein-drug binding free energy calculations using distributed computing / Morgan Lawrenz [and others] -- Free energy calculations from one-step perturbations / Chris Oostenbrink -- Using metadynamics and path collective variables to study ligand binding and induced conformational transitions / Neva Bešker and Francesco L. Gervasio -- Accelerated molecular dynamics in computational drug design / Jeff Wereszczynski and J. Andrew McCammon -- Molecular dynamics applied in drug discovery : the case of HIV-1 protease / Yi Shang and Carlos Simmerling -- Decomposing the energetic impact of drug-resistant mutations : the example of HIV-1 protease-DRV binding / Yufeng Cai and Celia Schiffer -- Guide to virtual screening : application to the Akt phosphatase PHLPP / William Sinko [and others] -- Molecular-level simulation of pandemic influenza glycoproteins / Rommie E. Amaro and Wilfred W. Li -- Homology modeling of cannabinoid receptors : discovery of cannabinoid analogues for therapeutic use / Chia-en A. Chang [and others] -- High-throughput virtual screening lead to discovery of non-peptidic inhibitors of West Nile virus NS3 protease / Danzhi Huang.

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 BiologyïÃ,¿Ã,½ 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.