Description
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. 1. Molecular Dynamics Simulations and Computer-Aided Drug Discovery Ryan C. Godwin, Ryan Melvin, and Freddie R. Salsbury, Jr. 2. A Review of Evolutionary Algorithms for Computing Functional Conformations of Protein Molecules Amarda Shehu 3. Incorporating Receptor Flexibility into Structure-Based Drug Discovery Chung F. Wong 4. Understanding Water and Its Many Roles in Biological Structure: Ways to Exploit a Resource for Drug Discovery Mostafa H. Ahmed, Alessio Amadasi, Alexander S. Bayden, Derek J. Cashman, Pietro Cozzini, Chenxiao Da, Deliang L. Chen, Micaela Fornabaio, Vishal N. Koparde, Andrea Mozzarelli, Hardik I. Parikh, Aurijit Sarkar, J. Neel Scarsdale, Francesca Spyrakis, J. Andrew Surface, Ashutosh Tripathi, Saheem A. Zaidi, and Glen E. Kellogg 5. CAVITY: Mapping the Druggable Binding Site Weilin Zhang, Yaxia Yuan, Jianfeng Pei, and Luhua Lai 6. Methods for Detecting Protein Binding Interfaces Nurit Haspel 7. MDock: An Ensemble Docking Suite for Molecular Docking, Scoring, and In Silico Screening Chengfei Yan and Xiaoqin Zou 8. Pharmacophore Modeling: Methods and Applications David Ryan Koes 9. Computational Fragment-Based Drug Design Chunquan Sheng, Guoqiang Dong, and Chen Wang 10. Applications of the Fragment Molecular Orbital Method to Drug Research Michael P. Mazanetz, Ewa Chudyk, Dmitri G. Fedorov, and Yuri Alexeev 11. Recent Advances in the Open Access Cheminformatics Toolkits, Software Tools, Workflow Environments, and Databases Pravin Ambure, Rahul Balasaheb Aher, and Kunal Roy
