Molecular Docking For Computer Aided Drug Design

Molecular Docking for Computer-Aided Drug Design: Fundamentals, Techniques, Resources and Applications offers in-depth coverage on the use of molecular docking for drug design. The book is divided into three main sections that cover basic techniques, tools, web servers and applications. It is an essential reference for students and researchers involved in drug design and discovery. Covers the latest information and state-of-the-art trends in structure-based drug design methodologies Includes case studies that complement learning Consolidates fundamental concepts and current practice of molecular docking into one convenient resource

This book provides up-to-date information on bioinformatics tools for the discovery and development of new drug molecules. It discusses a range of computational applications, including three-dimensional modeling of protein structures, protein-ligand docking, and molecular dynamics simulation of protein-ligand complexes for identifying desirable drug candidates. It also explores computational approaches for identifying potential drug targets and for pharmacophore modeling. Moreover, it presents structure- and ligand-based drug design tools to optimize known drugs and guide the design of new molecules. The book also describes methods for identifying small-molecule binding pockets in proteins, and summarizes the databases used to explore the essential properties of drugs, drug-like small molecules and their targets. In addition, the book highlights various tools to predict the absorption, distribution, metabolism, excretion (ADME) and toxicity (T) of potential drug candidates. Lastly, it reviews in silico tools that can facilitate vaccine design and discusses their limitations.

Bioinformatics allows researchers to answer biological questions with advanced computational methods which involves the application of statistics and mathematical modeling. Structural bioinformatics enables the prediction and analysis of 3D structures of macromolecules while Computer Aided Drug Designing (CADD) assists scientists to design effective active molecules against diseases. However, the concepts in structural bioinformatics and CADD can be complex to understand for students and educated laymen. This quick guideline is intended as a basic manual for beginner students and instructors involved in bioinformatics and computational chemistry courses. Readers will learn the basics of structural bioinformatics, primary and secondary analysis and prediction, structural visualization, structural analysis and molecular docking. The book provides the reader an easy to read summary of the tools and techniques in structural bioinformatics as well as their limitations. In this revised edition, the authors have updated information in a number of chapters with a specific focus on the section on protein structure visualization and evaluation. Additional information on protein-ligand interaction studies has also been provided in this new edition. Therefore, the book is a useful handbook for aspiring scholars who wish to learn the basic concepts in computational analysis of biomolecules.

As the pharmaceutical industry continues to advance, new techniques in drug design are emerging. In order to deliver optimum care to patients, the development of innovative pharmacological techniques has become a widely studied topic. Applied Case Studies and Solutions in Molecular Docking-Based Drug Design is a pivotal reference source for the latest scholarly research on the progress of pharmaceutical design and computational approaches in the field of molecular docking. Highlighting innovative research perspectives and real-world applications, this book is ideally designed for professionals, researchers, practitioners, and medical chemists actively involved in computational chemistry and pharmaceutical sciences.

The role of technology in the medical field has resulted in significant developments within the pharmaceutical industry. Computational approaches have emerged as a crucial method in further advancing drug design and development. Methods and Algorithms for Molecular Docking-Based Drug Design and Discovery presents emerging research on the application of computer-assisted design methods for drugs, emphasizing the benefits and improvements that molecular docking has caused within the pharmaceutical industry. Focusing on validation methods, search algorithms, and scoring functions, this book is a pivotal resource for professionals, researchers, students, and practitioners in the field of theoretical and computational chemistry.

This second edition provides new and updated methods and techniques for identification of drug target, binding sites prediction, high- throughput virtual screening, lead discovery and optimization, conformational sampling, prediction of pharmacokinetic properties using computer-based methodologies. Chapters also focus on the application of the latest artificial intelligence technologies for computer aided drug discovery. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary methods, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Computational Drug Discovery and Design, Second Edition aims to effectively utilize computational methodologies in discovery and design of novel drugs.

Concepts and Experimental Protocols of Modelling and Informatics in Drug Design discusses each experimental protocol utilized in the field of bioinformatics, focusing especially on computer modeling for drug development. It helps the user in understanding the field of computer-aided molecular modeling (CAMM) by presenting solved exercises and examples. The book discusses topics such as fundamentals of molecular modeling, QSAR model generation, protein databases and how to use them to select and analyze protein structure, and pharmacophore modeling for drug targets. Additionally, it discusses data retrieval system, molecular surfaces, and freeware and online servers. The book is a valuable source for graduate students and researchers on bioinformatics, molecular modeling, biotechnology and several members of biomedical field who need to understand more about computer-aided molecular modeling. Presents exercises with solutions to aid readers in validating their own protocol Brings a thorough interpretation of results of each exercise to help readers compare them to their own study Explains each parameter utilized in the algorithms to help readers understand and manipulate various features of molecules and target protein to design their study

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.