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Molecular Docking for Computer-Aided Drug Design

Molecular Docking for Computer-Aided Drug Design
  • Author : Mohane S. Coumar
  • Publisher :Unknown
  • Release Date :2021-03-01
  • Total pages :520
  • ISBN : 9780128223130
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Summary : 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

Molecular Docking for Computer-Aided Drug Design

Molecular Docking for Computer-Aided Drug Design
  • Author : Mohane S. Coumar
  • Publisher :Unknown
  • Release Date :2021-03-15
  • Total pages :520
  • ISBN : 9780128223123
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Summary : 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

Computer-Aided Drug Design

Computer-Aided Drug Design
  • Author : Dev Bukhsh Singh
  • Publisher :Unknown
  • Release Date :2020-10-09
  • Total pages :306
  • ISBN : 9789811568152
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Summary : 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.

Applied Case Studies and Solutions in Molecular Docking-Based Drug Design

Applied Case Studies and Solutions in Molecular Docking-Based Drug Design
  • Author : Dastmalchi, Siavoush
  • Publisher :Unknown
  • Release Date :2016-05-11
  • Total pages :367
  • ISBN : 9781522503637
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Summary : 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.

Methods and Algorithms for Molecular Docking-Based Drug Design and Discovery

Methods and Algorithms for Molecular Docking-Based Drug Design and Discovery
  • Author : Dastmalchi, Siavoush
  • Publisher :Unknown
  • Release Date :2016-05-03
  • Total pages :456
  • ISBN : 9781522501169
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Summary : 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.

Quick Guideline for Computational Drug Design

Quick Guideline for Computational Drug Design
  • Author : Sheikh Arslan Sehgal, A. Hammad Mirza,Rana Adnan Tahir,Asif Mir
  • Publisher :Unknown
  • Release Date :2018-02-16
  • Total pages :151
  • ISBN : 9781681086033
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Summary : 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. Therefore, the book is a useful handbook for aspiring scholars who wish to learn the basic concepts in computational analysis of biomolecules.

Computer-Aided Drug Discovery

Computer-Aided Drug Discovery
  • Author : Wei Zhang
  • Publisher :Unknown
  • Release Date :2016-06-07
  • Total pages :305
  • ISBN : 1493935194
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Summary : 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.

Protein Modelling

Protein Modelling
  • Author : Andrew Gamble
  • Publisher :Unknown
  • Release Date :2014-11-13
  • Total pages :329
  • ISBN : 9783319099767
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Summary : In this volume, a detailed description of cutting-edge computational methods applied to protein modeling as well as specific applications are presented. Chapters include: the application of Car-Parrinello techniques to enzyme mechanisms, the outline and application of QM/MM methods, polarizable force fields, recent methods of ligand docking, molecular dynamics related to NMR spectroscopy, computer optimization of absorption, distribution, metabolism and excretion extended by toxicity for drugs, enzyme design and bioinformatics applied to protein structure prediction. A keen emphasis is laid on the clear presentation of complex concepts, since the book is primarily aimed at Ph.D. students, who need an insight in up-to-date protein modeling. The inclusion of descriptive, color figures will allow the reader to get a pictorial representation of complicated structural issues.

Guidebook on Molecular Modeling in Drug Design

Guidebook on Molecular Modeling in Drug Design
  • Author : N. Claude Cohen
  • Publisher :Unknown
  • Release Date :1996-05-10
  • Total pages :361
  • ISBN : 012178245X
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Summary : The molecular modeling perspective in drug design. (N. Calude Cohen). Molecular graphics and modeling: tools of the trade. (Roderick E. Hubbard). Molecular modeling of small molecules. (Tamara Gund). Computer assisted new lead design. (Akiko Itai, Miho Yamada Mizutani, Yoshihiko Nishibata, and Nubuo Tomioka). Experimental techniques and data banks. (John P. Priestle and C. Gregory Paris). Computer-assisted drug discovery. (Peter Gund, Gerald Maggiora, and James P. Snyder). Modeling drug-receptor interactions. (Konrad F. Koehler, Shashidhar N. Rao, and James P. Snyder). Glossary of terminology. (J. P. Tollenaere).

Computational Drug Discovery and Design

Computational Drug Discovery and Design
  • Author : Mohini Gore,Umesh B. Jagtap
  • Publisher :Unknown
  • Release Date :2019-04-12
  • Total pages :488
  • ISBN : 1493992767
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Summary : This volume details methods and techniques for identification of drug targets, binding sites prediction, high-throughput virtual screening,and prediction of pharmacokinetic properties using computer based methodologies. Chapters guide readers through techniques of the available computational tools, developing prediction models for drug target prediction and de novo design of ligands, structure based drug designing, fragment-based drug designing, molecular docking, and scoring functions for assessing protein-ligand docking protocols. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials, step-by-step, readily reproducible protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Computational Drug Discovery and Design aims to provide protocols for the use of bioinformatics tools in drug discovery and design.

Drug Design

Drug Design
  • Author : Kenneth M. Merz, Jr,Dagmar Ringe,Charles H. Reynolds
  • Publisher :Unknown
  • Release Date :2010-05-31
  • Total pages :274
  • ISBN : 9780521887236
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Summary : This book provides a complete snapshot of various experimental approaches to structure-based and ligand-based drug design and is illustrated with more than 200 images.

Computational Drug Discovery and Design

Computational Drug Discovery and Design
  • Author : Riccardo Baron
  • Publisher :Unknown
  • Release Date :2011-12-23
  • Total pages :628
  • ISBN : 1617794643
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Summary : Due to the rapid and steady growth of available low-cost computer power, the use of computers for discovering and designing new drugs is becoming a central topic in modern molecular biology and medicinal chemistry. In Computational Drug Discovery and Design: Methods and Protocols expert researchers in the field provide key techniques to investigate biomedical applications for drug developments based on computational chemistry. These include methods and techniques from binding sites prediction to the accurate inclusion of solvent and entropic effects, from high-throughput screening of large compound databases to the expanding area of protein-protein inhibition, toward quantitative free-energy approaches in ensemble-based drug design using distributed computing. Written in the highly successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective topics, reference to software and open source analysis tools, step-by-step, readily reproducible computational protocols, and key tips on troubleshooting and avoiding known pitfalls. Thorough and intuitive, Computational Drug Discovery and Design: Methods and Protocols aids scientists in the continuing study of state-of-the-art concepts and computer-based methodologies.

Molecular Docking

Molecular Docking
  • Author : Dimitrios Vlachakis
  • Publisher :Unknown
  • Release Date :2018-07-11
  • Total pages :188
  • ISBN : 9781789233544
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Summary : Molecular docking has always been and will be on the forefront of developments in the eminent field of drug design and medicinal chemistry. At the early days, drug discovery was based on blackboard drawings and expert intuition. However, as times move on, the amount of available information and overall knowledge base that needs to be analyzed cannot be processed manually. This, coupled by the rapid growth in computational infrastructure and processing power, has allowed for the efficient use of molecular docking tools and algorithms to be considered in the greater field of drug discovery. In the postgenomic era, molecular docking has become the key player for the screening of hundreds of thousands of compounds against a repertoire of pharmacological targets.

Bioinformatics Techniques for Drug Discovery

Bioinformatics Techniques for Drug Discovery
  • Author : Aman Chandra Kaushik,Ajay Kumar,Shiv Bharadwaj,Ravi Chaudhary,Shakti Sahi
  • Publisher :Unknown
  • Release Date :2018-04-25
  • Total pages :57
  • ISBN : 9783319757322
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Summary : The application of bioinformatics approaches in drug design involves an interdisciplinary array of sophisticated techniques and software tools to elucidate hidden or complex biological data. This work reviews the latest bioinformatics approaches used for drug discovery. The text covers ligand-based and structure-based approaches for computer-aided drug design, 3D pharmacophore modeling, molecular dynamics simulation, the thermodynamics of ligand−receptor and ligand−enzyme association, thermodynamic characterization and optimization, and techniques for computational genomics and proteomics.

In Silico Drug Discovery and Design

In Silico Drug Discovery and Design
  • Author : Claudio N. Cavasotto
  • Publisher :Unknown
  • Release Date :2015-08-06
  • Total pages :558
  • ISBN : 9781482217858
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Summary : In Silico Drug Discovery and Design: Theory, Methods, Challenges, and Applications provides a comprehensive, unified, and in-depth overview of the current methodological strategies in computer-aided drug discovery and design. Its main aims are to introduce the theoretical framework and algorithms, discuss the range of validity, strengths and limita

Innovations and Implementations of Computer Aided Drug Discovery Strategies in Rational Drug Design

Innovations and Implementations of Computer Aided Drug Discovery Strategies in Rational Drug Design
  • Author : Sanjeev Kumar Singh
  • Publisher :Unknown
  • Release Date :2021
  • Total pages :229
  • ISBN : 9789811589362
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Summary :

Molecular Modeling in Drug Design

Molecular Modeling in Drug Design
  • Author : Rebecca Wade,Outi Salo-Ahen
  • Publisher :Unknown
  • Release Date :2019-03-26
  • Total pages :220
  • ISBN : 9783038976141
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Summary : Since the first attempts at structure-based drug design about four decades ago, molecular modelling techniques for drug design have developed enormously, along with the increasing computational power and structural and biological information of active compounds and potential target molecules. Nowadays, molecular modeling can be considered to be an integral component of the modern drug discovery and development toolbox. Nevertheless, there are still many methodological challenges to be overcome in the application of molecular modeling approaches to drug discovery. The eight original research and five review articles collected in this book provide a snapshot of the state-of-the-art of molecular modeling in drug design, illustrating recent advances and critically discussing important challenges. The topics covered include virtual screening and pharmacophore modelling, chemoinformatic applications of artificial intelligence and machine learning, molecular dynamics simulation and enhanced sampling to investigate contributions of molecular flexibility to drug–receptor interactions, the modeling of drug–receptor solvation, hydrogen bonding and polarization, and drug design against protein–protein interfaces and membrane protein receptors.

Chemometrics Applications and Research

Chemometrics Applications and Research
  • Author : Andrew G. Mercader,Pablo R. Duchowicz,P. M. Sivakumar
  • Publisher :Unknown
  • Release Date :2016-03-30
  • Total pages :458
  • ISBN : 9781498722599
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Summary : This important new book provides innovative material, including peer-reviewed chapters and survey articles on new applied research and development, in the scientifically important field of QSAR in medicinal chemistry. QSAR is a growing field because available computing power is continuously increasing, QSAR’s potential is enormous, limited only by the quantity and quality of the available experimental input, which are also continuously improving. The number of possible structures for the design of new organic compounds is difficult to imagine, and QSAR helps to predict their activities even before synthesis. The book provides a wealth of valuable information and: • Presents an overview of recent developments in QSAR methodologies along with a brief history of QSAR • Covers the available web resource tools and in silico techniques used in virtual screening and drug discovery processes, compiling an extensive review of web resources in the following categories: databases related to chemical compounds, drug targets, and ADME/toxicity prediction; molecular modeling and drug designing; virtual screening; pharmacophore generation; molecular descriptor calculation software; software for quantum mechanics; ligand binding affinities (docking); and software related to ADME/toxicity prediction • Reviews the rm2 as a more stringent measure for the assessment of model predictivity compared to traditional validation metrics, being specifically important since validation is a crucial step in any QSAR study • Presents linear model improvement techniques that take into account the conformation flexibility of the modeled molecules • Summarizes the building processes of four different pharmacophore models: common-feature, 3D-QSAR, protein-, and protein-ligand complexes • Shows the role of different conceptual density functional theory based chemical reactivity descriptors, such as hardness, electrophilicity, net electrophilicity, and philicity in the design of different QSAR/QSPR/QSTR models • Reviews the use of chemometrics in PPAR research highlighting its substantial contribution in identifying essential structural characteristics and understanding the mechanism of action • Presents the structures and QSARs of antimicrobial and immunosuppressive cyclopeptides, discussing the balance of antimicrobial and haemolytic activities for designing new antimicrobial cyclic peptides • Shows the relationship between DFT global descriptors and experimental toxicity of a selected group of polychlorinated biphenyls, exploring the efficacy of three DFT descriptors • Reviews the applications of Quantitative Structure-Relative Sweetness Relationships (QSRSR), showing that the last decade was marked by an increase in the number of studies regarding QSAR applications for both understanding the sweetness mechanism and synthesizing novel sweetener compounds for the food additive industry The wide coverage makes this book an excellent reference for those in chemistry, pharmacology, and medicine as well as for research centers, governmental organizations, pharmaceutical companies, and health and environmental control organizations.

Free Energy Calculations

Free Energy Calculations
  • Author : Christophe Chipot,Andrew Pohorille
  • Publisher :Unknown
  • Release Date :2007-01-08
  • Total pages :517
  • ISBN : 9783540384472
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Summary : Presenting an account of the concepts that underly different approaches devised for the determination of free energies, this book aims to give the reader, an insight into the theoretical and computational foundations of the subject. It is aimed at students and researchers having a background in chemistry, physics, engineering and physical biology.

Computational Drug Design

Computational Drug Design
  • Author : D. C. Young
  • Publisher :Unknown
  • Release Date :2009-01-28
  • Total pages :344
  • ISBN : 047045184X
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Summary : Helps you choose the right computational tools and techniques to meet your drug design goals Computational Drug Design covers all of the major computational drug design techniques in use today, focusing on the process that pharmaceutical chemists employ to design a new drug molecule. The discussions of which computational tools to use and when and how to use them are all based on typical pharmaceutical industry drug design processes. Following an introduction, the book is divided into three parts: Part One, The Drug Design Process, sets forth a variety of design processes suitable for a number of different drug development scenarios and drug targets. The author demonstrates how computational techniques are typically used during the design process, helping readers choose the best computational tools to meet their goals. Part Two, Computational Tools and Techniques, offers a series of chapters, each one dedicated to a single computational technique. Readers discover the strengths and weaknesses of each technique. Moreover, the book tabulates comparative accuracy studies, giving readers an unbiased comparison of all the available techniques. Part Three, Related Topics, addresses new, emerging, and complementary technologies, including bioinformatics, simulations at the cellular and organ level, synthesis route prediction, proteomics, and prodrug approaches. The book's accompanying CD-ROM, a special feature, offers graphics of the molecular structures and dynamic reactions discussed in the book as well as demos from computational drug design software companies. Computational Drug Design is ideal for both students and professionals in drug design, helping them choose and take full advantage of the best computational tools available. Note: CD-ROM/DVD and other supplementary materials are not included as part of eBook file.

Antiviral computer-aided drug design

Antiviral computer-aided drug design
  • Author : DIMITRIOS VLACHAKIS
  • Publisher :Unknown
  • Release Date :2012
  • Total pages :229
  • ISBN : 9781300229742
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Summary :