Molecular Dynamics Simulations and Computer-Aided Drug Discovery -- A Review of Evolutionary Algorithms for Computing Functional Conformations of Protein Molecules -- Incorporating Receptor Flexibility into Structure-Based Drug Discovery -- Understanding Water and Its Many Roles in Biological Structure: Ways to Exploit a Resource for Drug Discovery -- CAVITY: Mapping the Druggable Binding Site -- Methods for Detecting Protein Binding Interfaces -- MDock: An Ensemble Docking Suite for Molecular Docking, Scoring, and In Silico Screening -- Pharmacophore Modeling: Methods and Applications -- Computational Fragment-Based Drug Design -- Applications of the Fragment Molecular Orbital Method to Drug Research -- Recent Advances in the Open Access Cheminformatics Toolkits, Software Tools, Workflow Environments, and Databases.

This detailed volume examines computer-aided drug discovery (CADD), a crucial component of modern drug discovery programs that is widely utilized to identity and optimize bioactive compounds for the development of new drugs. With a focus on the methods that are commonly used in the early stage of drug discovery, chapters explore computer simulation, structure prediction, conformational sampling, binding site mapping, docking and scoring, in silico screening, and fragment-based drug design. In addition to the state-of-the-art theoretical concept, this book also includes step-by-step, readily reproducible computational protocols as well as examples of various CADD strategies. The limitations and potential pitfalls of different computational methods are discussed by experts, and tips and advice for their applications are suggested. Practical and thorough, Computer-Aided Drug Discovery serves as an ideal addition to the Methods in Pharmacology and Toxicology series, guiding researchers toward their lab's goals with this exciting and versatile technology.