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E-raamat: Computer-Aided Drug Discovery

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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 labs goals with this exciting and versatile technology.
Preface v
Contributors ix
Molecular Dynamics Simulations and Computer-Aided Drug Discovery
1(30)
Ryan C. Godwin
Ryan Melvin
Freddie R. Salsbury Jr.
A Review of Evolutionary Algorithms for Computing Functional Conformations of Protein Molecules
31(34)
Amarda Shehu
Incorporating Receptor Flexibility into Structure-Based Drug Discovery
65(20)
Chung F. Wong
Understanding Water and Its Many Roles in Biological Structure: Ways to Exploit a Resource for Drug Discovery
85(26)
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
Glen E. Kellogg
CAVITY: Mapping the Druggable Binding Site
111(22)
Weilin Zhang
Yaxia Yuan
Jianfeng Pei
Luhua Lai
Methods for Detecting Protein Binding Interfaces
133(20)
Nurit Haspel
MDock: An Ensemble Docking Suite for Molecular Docking, Scoring and In Silico Screening
153(14)
Chengfei Yan
Xiaoqin Zou
Pharmacophore Modeling: Methods and Applications
167(22)
David Ryan Koes
Computational Fragment-Based Drug Design
189(28)
Chunquan Sheng
Guoqiang Dong
Chen Wang
Applications of the Fragment Molecular Orbital Method to Drug Research
217(40)
Michael P. Mazanetz
Ewa Chudyk
Dmitri G. Fedorov
Yuri Alexeev
Recent Advances in the Open Access Cheminformatics Toolkits, Software Tools, Workflow Environments, and Databases
257(40)
Pravin Ambure
Rahul Balasaheb Aher
Kunal Roy
Index 297