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 ... [et al.] -- Information entropic functions for molecular descriptor profiling / Anne Mai Wassermann ... [et al.] -- Expanding the conformational selection paradigm in protein-ligand docking / Guray Kuzu ... [et al.] -- 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 ... [et al.] -- 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 ... [et al.] -- ATTRACT and PTOOLS : open source programs for protein-protein docking Sebastian Schneider ... [et al.] -- 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 ... [et al.] -- 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 ... [et al.] -- 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 ... [et al.] -- 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 ... [et al.] -- 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 ... [et al.] -- High-throughput virtual screening lead to discovery of non-peptidic inhibitors of West Nile virus NS3 protease / Danzhi Huang.
Series:
Methods in molecular biology, 1064-3745 ; 819 Springer protocols
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