Computational drug discovery and design
By: edited by Riccardo Baron
Series: Methods in molecular biology -- 819; Springer protocols; Methods in molecular biology (Clifton, N.J.) -- v. 819.; Springer protocols
Publisher: Humana Press
Published: 2012
Place of publication: New York
Language: eng
Number of pages: 628
ISBN-13: 9781617794643; 9781617794650
Subjects: Laboratory Manuals; Methods; Computational Biology; Drugs; Drug development; Drug Design; Design; Computer-Aided Design; Drug Discovery; Laboratory manuals
Notes: Includes bibliographical references and index.
Table of contents: title: A molecular dynamics ensemble-based approach for the mapping of druggable binding sites / Anthony Ivetac and J. Andrew McCammon; title: Analysis of protein binding sites by computational solvent mapping / David R. Hall, Dima Kozakov, and Sandor Vajda; title: Evolutionary trace for prediction and redesign of protein functional sites / Angela Wilkins ... [et al.]; title: Information entropic functions for molecular descriptor profiling /  Anne Mai Wassermann ... [et al.]; title: Expanding the conformational selection paradigm in protein-ligand docking / Guray Kuzu ... [et al.]; title: Flexibility analysis of biomacromolecules with application to computer-aided drug design / Simone Fulle and Holger Gohlke; title: On the use of molecular dynamics receptor conformations for virtual screening / Sara E. Nichols, Riccardo Baron, and J. Andrew McCammon; title: Virtual ligand screening against comparative protein structure models / Hao Fan, John J. Irwin, and Andrej Sali; title: AMMOS software : method and application / Tania Pencheva ... [et al.]; title: Rosetta ligand docking with flexible XML protocols / Gordon Lemmon and Jens Meiler; title: Normal mode-based approaches in receptor ensemble docking / Claudio N. Cavasotto; title: Application of conformational clustering in protein-ligand docking / Giovanni Bottegoni, Walter Rocchia, and Andrea Cavalli; title: How to benchmark methods for structure-based virtual screening of large compound libraries / Andrew J. Christofferson and Niu Huang; title: AGGRESCAN : method, application, and perspectives for drug design / Natalia S. de Groot ... [et al.]; title: ATTRACT and PTOOLS : open source programs for protein-protein docking Sebastian Schneider ... [et al.]; title: Prediction of interacting protein residues using sequence and structure data / Vedran Franke, Mile Šikić, and Kristian Vlahoviček; title: MM-GB/SA rescoring of docking poses / Cristiano R.W. Guimarães; title: A case study of scoring and rescoring in peptide docking / Zunnan Huang and Chung F. Wong; title: The solvated interaction energy method for scoring binding affinities / Traian Sulea and Enrico O. Purisima; title: Linear interaction energy : method and applications in drug design / Hugo Guitiérrez-de-Terán and Johan Åqvist; title: Estimation of conformational entropy in protein-ligand interactions : a computational perspective / Anton A. Polyansky, Ruben Zubac, and Bojan Zagrovic; title: 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; title: Protein-water interactions in MD simulations : POPS/POPSCOMP solvent accessibility analysis, solvation forces and hydration sites / Arianna Fornili ... [et al.]; title: Computing the thermodynamic contributions of interfacial water / Zheng Li and Themis Lazaridis; title: Assignment of protonation states in proteins and ligands : combining pKa prediction with hydrogen bonding network optimization / Elmar Krieger ... [et al.]; title: Best practices in free energy calculations for drug design / Michael R. Shirts; title: Independent-trajectory thermodynamic integration : a practical guide to protein-drug binding free energy calculations using distributed computing / Morgan Lawrenz ... [et al.]; title: Free energy calculations from one-step perturbations / Chris Oostenbrink; title: Using metadynamics and path collective variables to study ligand binding and induced conformational transitions / Neva Bešker and Francesco L. Gervasio; title: Accelerated molecular dynamics in computational drug design / Jeff Wereszczynski and J. Andrew McCammon; title: Molecular dynamics applied in drug discovery : the case of HIV-1 protease / Yi Shang and Carlos Simmerling; title: Decomposing the energetic impact of drug-resistant mutations : the example of HIV-1 protease-DRV binding / Yufeng Cai and Celia Schiffer; title: Guide to virtual screening : application to the Akt phosphatase PHLPP / William Sinko ... [et al.]; title: Molecular-level simulation of pandemic influenza glycoproteins / Rommie E. Amaro and Wilfred W. Li; title: Homology modeling of cannabinoid receptors : discovery of cannabinoid analogues for therapeutic use / Chia-en A. Chang ... [et al.]; title: High-throughput virtual screening lead to discovery of non-peptidic inhibitors of West Nile virus NS3 protease / Danzhi Huang.