Computer-Aided Drug Discovery

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