Pharmacophore Perception, Development, and Use in Drug Design

Pharmacophore Perception, Development, and Use in Drug Design

Author: Osman F. Güner

Publisher: Internat'l University Line

Published: 2000

Total Pages: 598

ISBN-13: 9780963681768

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In the early 1900s, Paul Ehrlich first defined pharmacophores as molecule frameworks that carry the essential features responsible for a drug's biological activity, and the modern definition is little changed. The 27 studies here begin by tracing the evolution of the concept in pharmaceutical research, then cover analog-based and receptor-based varieties, new algorithms, and the future of research. Among the specific topics: pharmacophores based on multiple common-feature alignments; modeling programs including HypoGen, DISCO, Catalyst, HipHop, GASP, Chem-X, Apex-3D, CoMFA; pharmacophore-based molecular docking, a technique for developing a pharmacophore model that accommodates inherent protein flexibility; and the effect of variable weights and tolerances on predictive model generation. Books in Print lists only one other book on the topic of pharmacophores. Annotation copyrighted by Book News, Inc., Portland, OR


Book Synopsis Pharmacophore Perception, Development, and Use in Drug Design by : Osman F. Güner

Download or read book Pharmacophore Perception, Development, and Use in Drug Design written by Osman F. Güner and published by Internat'l University Line. This book was released on 2000 with total page 598 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the early 1900s, Paul Ehrlich first defined pharmacophores as molecule frameworks that carry the essential features responsible for a drug's biological activity, and the modern definition is little changed. The 27 studies here begin by tracing the evolution of the concept in pharmaceutical research, then cover analog-based and receptor-based varieties, new algorithms, and the future of research. Among the specific topics: pharmacophores based on multiple common-feature alignments; modeling programs including HypoGen, DISCO, Catalyst, HipHop, GASP, Chem-X, Apex-3D, CoMFA; pharmacophore-based molecular docking, a technique for developing a pharmacophore model that accommodates inherent protein flexibility; and the effect of variable weights and tolerances on predictive model generation. Books in Print lists only one other book on the topic of pharmacophores. Annotation copyrighted by Book News, Inc., Portland, OR

Applied Chemoinformatics

Applied Chemoinformatics

Author: Thomas Engel

Publisher: John Wiley & Sons

Published: 2018-06-05

Total Pages: 660

ISBN-13: 352734201X

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Edited by world-famous pioneers in chemoinformatics, this is a clearly structured and applications-oriented approach to the topic, providing up-to-date and focused information on the wide range of applications in this exciting field. The authors explain methods and software tools, such that the reader will not only learn the basics but also how to use the different software packages available. Experts describe applications in such different fields as structure-spectra correlations, virtual screening, prediction of active sites, library design, the prediction of the properties of chemicals, the development of new cosmetics products, quality control in food, the design of new materials with improved properties, toxicity modeling, assessment of the risk of chemicals, and the control of chemical processes. The book is aimed at advanced students as well as lectures but also at scientists that want to learn how chemoinformatics could assist them in solving their daily scientific tasks. Together with the corresponding textbook Chemoinformatics - Basic Concepts and Methods (ISBN 9783527331093) on the fundamentals of chemoinformatics readers will have a comprehensive overview of the field.


Book Synopsis Applied Chemoinformatics by : Thomas Engel

Download or read book Applied Chemoinformatics written by Thomas Engel and published by John Wiley & Sons. This book was released on 2018-06-05 with total page 660 pages. Available in PDF, EPUB and Kindle. Book excerpt: Edited by world-famous pioneers in chemoinformatics, this is a clearly structured and applications-oriented approach to the topic, providing up-to-date and focused information on the wide range of applications in this exciting field. The authors explain methods and software tools, such that the reader will not only learn the basics but also how to use the different software packages available. Experts describe applications in such different fields as structure-spectra correlations, virtual screening, prediction of active sites, library design, the prediction of the properties of chemicals, the development of new cosmetics products, quality control in food, the design of new materials with improved properties, toxicity modeling, assessment of the risk of chemicals, and the control of chemical processes. The book is aimed at advanced students as well as lectures but also at scientists that want to learn how chemoinformatics could assist them in solving their daily scientific tasks. Together with the corresponding textbook Chemoinformatics - Basic Concepts and Methods (ISBN 9783527331093) on the fundamentals of chemoinformatics readers will have a comprehensive overview of the field.

Tutorials in Chemoinformatics

Tutorials in Chemoinformatics

Author: Alexandre Varnek

Publisher: John Wiley & Sons

Published: 2017-06-22

Total Pages: 488

ISBN-13: 1119137985

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30 tutorials and more than 100 exercises in chemoinformatics, supported by online software and data sets Chemoinformatics is widely used in both academic and industrial chemical and biochemical research worldwide. Yet, until this unique guide, there were no books offering practical exercises in chemoinformatics methods. Tutorials in Chemoinformatics contains more than 100 exercises in 30 tutorials exploring key topics and methods in the field. It takes an applied approach to the subject with a strong emphasis on problem-solving and computational methodologies. Each tutorial is self-contained and contains exercises for students to work through using a variety of software packages. The majority of the tutorials are divided into three sections devoted to theoretical background, algorithm description and software applications, respectively, with the latter section providing step-by-step software instructions. Throughout, three types of software tools are used: in-house programs developed by the authors, open-source programs and commercial programs which are available for free or at a modest cost to academics. The in-house software and data sets are available on a dedicated companion website. Key topics and methods covered in Tutorials in Chemoinformatics include: Data curation and standardization Development and use of chemical databases Structure encoding by molecular descriptors, text strings and binary fingerprints The design of diverse and focused libraries Chemical data analysis and visualization Structure-property/activity modeling (QSAR/QSPR) Ensemble modeling approaches, including bagging, boosting, stacking and random subspaces 3D pharmacophores modeling and pharmacological profiling using shape analysis Protein-ligand docking Implementation of algorithms in a high-level programming language Tutorials in Chemoinformatics is an ideal supplementary text for advanced undergraduate and graduate courses in chemoinformatics, bioinformatics, computational chemistry, computational biology, medicinal chemistry and biochemistry. It is also a valuable working resource for medicinal chemists, academic researchers and industrial chemists looking to enhance their chemoinformatics skills.


Book Synopsis Tutorials in Chemoinformatics by : Alexandre Varnek

Download or read book Tutorials in Chemoinformatics written by Alexandre Varnek and published by John Wiley & Sons. This book was released on 2017-06-22 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt: 30 tutorials and more than 100 exercises in chemoinformatics, supported by online software and data sets Chemoinformatics is widely used in both academic and industrial chemical and biochemical research worldwide. Yet, until this unique guide, there were no books offering practical exercises in chemoinformatics methods. Tutorials in Chemoinformatics contains more than 100 exercises in 30 tutorials exploring key topics and methods in the field. It takes an applied approach to the subject with a strong emphasis on problem-solving and computational methodologies. Each tutorial is self-contained and contains exercises for students to work through using a variety of software packages. The majority of the tutorials are divided into three sections devoted to theoretical background, algorithm description and software applications, respectively, with the latter section providing step-by-step software instructions. Throughout, three types of software tools are used: in-house programs developed by the authors, open-source programs and commercial programs which are available for free or at a modest cost to academics. The in-house software and data sets are available on a dedicated companion website. Key topics and methods covered in Tutorials in Chemoinformatics include: Data curation and standardization Development and use of chemical databases Structure encoding by molecular descriptors, text strings and binary fingerprints The design of diverse and focused libraries Chemical data analysis and visualization Structure-property/activity modeling (QSAR/QSPR) Ensemble modeling approaches, including bagging, boosting, stacking and random subspaces 3D pharmacophores modeling and pharmacological profiling using shape analysis Protein-ligand docking Implementation of algorithms in a high-level programming language Tutorials in Chemoinformatics is an ideal supplementary text for advanced undergraduate and graduate courses in chemoinformatics, bioinformatics, computational chemistry, computational biology, medicinal chemistry and biochemistry. It is also a valuable working resource for medicinal chemists, academic researchers and industrial chemists looking to enhance their chemoinformatics skills.

The Ups and Downs in Drug Design

The Ups and Downs in Drug Design

Author: Victor E. Marquez

Publisher: CRC Press

Published: 2021-11-15

Total Pages: 566

ISBN-13: 1000462943

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The Ups and Downs in Drug Design: Adventures in Medicinal Chemistry highlights the necessity for an integrative approach in medicinal chemistry and chemical biology. As medicinal chemistry is not a monolithic science, it is important to emphasize the other various disciplines that are required for successful drug design. This book presents the author’s own personal experience in this field and describes the "ups" and "downs" that come with drug discovery. It is an excellent companion text for graduate and postgraduate students who would like further insight into the parameters of drug design, including the challenges that come with the project. Key Features Illustrates "real-life" examples in medicinal chemistry Integrates the use of physical, chemical, and biological concepts that are important in drug design Highlights the "ups" and "downs" that come with drug discovery Aims to inspire students who may be struggling with the challenges and thought process in drug design Intends to be an excellent companion text for graduate and postgraduate students


Book Synopsis The Ups and Downs in Drug Design by : Victor E. Marquez

Download or read book The Ups and Downs in Drug Design written by Victor E. Marquez and published by CRC Press. This book was released on 2021-11-15 with total page 566 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Ups and Downs in Drug Design: Adventures in Medicinal Chemistry highlights the necessity for an integrative approach in medicinal chemistry and chemical biology. As medicinal chemistry is not a monolithic science, it is important to emphasize the other various disciplines that are required for successful drug design. This book presents the author’s own personal experience in this field and describes the "ups" and "downs" that come with drug discovery. It is an excellent companion text for graduate and postgraduate students who would like further insight into the parameters of drug design, including the challenges that come with the project. Key Features Illustrates "real-life" examples in medicinal chemistry Integrates the use of physical, chemical, and biological concepts that are important in drug design Highlights the "ups" and "downs" that come with drug discovery Aims to inspire students who may be struggling with the challenges and thought process in drug design Intends to be an excellent companion text for graduate and postgraduate students

Computational Drug Design

Computational Drug Design

Author: D. C. Young

Publisher: John Wiley & Sons

Published: 2009-01-28

Total Pages: 344

ISBN-13: 9780470451847

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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.


Book Synopsis Computational Drug Design by : D. C. Young

Download or read book Computational Drug Design written by D. C. Young and published by John Wiley & Sons. This book was released on 2009-01-28 with total page 344 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Chemical and Structural Approaches to Rational Drug Design

Chemical and Structural Approaches to Rational Drug Design

Author: David B. Weiner

Publisher: CRC Press

Published: 2020-12-17

Total Pages: 291

ISBN-13: 1000099059

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This book is the first to provide both a broad overview of the current methodologies being applied to drug design and in-depth analyses of progress in specific fields. It details state-of-the-art approaches to pharmaceutical development currently used by some of the world's foremost laboratories. The book features contributors from a variety of fields, new techniques, previously unpublished data, and extensive reference lists.


Book Synopsis Chemical and Structural Approaches to Rational Drug Design by : David B. Weiner

Download or read book Chemical and Structural Approaches to Rational Drug Design written by David B. Weiner and published by CRC Press. This book was released on 2020-12-17 with total page 291 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is the first to provide both a broad overview of the current methodologies being applied to drug design and in-depth analyses of progress in specific fields. It details state-of-the-art approaches to pharmaceutical development currently used by some of the world's foremost laboratories. The book features contributors from a variety of fields, new techniques, previously unpublished data, and extensive reference lists.

SAR

SAR

Author: Eric J. Lien

Publisher: CRC Press

Published: 2020-09-11

Total Pages: 386

ISBN-13: 1000146898

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This book focuses on the quantitative structure-activity relationship of the disposition and activities of various pharmacological groups. It presents a systematic approach for linking different side effect of drugs to their molecular structure and physiochemical properties.


Book Synopsis SAR by : Eric J. Lien

Download or read book SAR written by Eric J. Lien and published by CRC Press. This book was released on 2020-09-11 with total page 386 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book focuses on the quantitative structure-activity relationship of the disposition and activities of various pharmacological groups. It presents a systematic approach for linking different side effect of drugs to their molecular structure and physiochemical properties.

Structural Bioinformatics: Applications in Preclinical Drug Discovery Process

Structural Bioinformatics: Applications in Preclinical Drug Discovery Process

Author: C. Gopi Mohan

Publisher: Springer

Published: 2019-01-10

Total Pages: 406

ISBN-13: 3030052826

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This book reviews the advances and challenges of structure-based drug design in the preclinical drug discovery process, addressing various diseases, including malaria, tuberculosis and cancer. Written by internationally recognized researchers, this edited book discusses how the application of the various in-silico techniques, such as molecular docking, virtual screening, pharmacophore modeling, molecular dynamics simulations, and residue interaction networks offers insights into pharmacologically active novel molecular entities. It presents a clear concept of the molecular mechanism of different drug targets and explores methods to help understand drug resistance. In addition, it includes chapters dedicated to natural-product- derived medicines, combinatorial drug discovery, the CryoEM technique for structure-based drug design and big data in drug discovery. The book offers an invaluable resource for graduate and postgraduate students, as well as for researchers in academic and industrial laboratories working in the areas of chemoinformatics, medicinal and pharmaceutical chemistry and pharmacoinformatics.


Book Synopsis Structural Bioinformatics: Applications in Preclinical Drug Discovery Process by : C. Gopi Mohan

Download or read book Structural Bioinformatics: Applications in Preclinical Drug Discovery Process written by C. Gopi Mohan and published by Springer. This book was released on 2019-01-10 with total page 406 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book reviews the advances and challenges of structure-based drug design in the preclinical drug discovery process, addressing various diseases, including malaria, tuberculosis and cancer. Written by internationally recognized researchers, this edited book discusses how the application of the various in-silico techniques, such as molecular docking, virtual screening, pharmacophore modeling, molecular dynamics simulations, and residue interaction networks offers insights into pharmacologically active novel molecular entities. It presents a clear concept of the molecular mechanism of different drug targets and explores methods to help understand drug resistance. In addition, it includes chapters dedicated to natural-product- derived medicines, combinatorial drug discovery, the CryoEM technique for structure-based drug design and big data in drug discovery. The book offers an invaluable resource for graduate and postgraduate students, as well as for researchers in academic and industrial laboratories working in the areas of chemoinformatics, medicinal and pharmaceutical chemistry and pharmacoinformatics.

3D QSAR in Drug Design

3D QSAR in Drug Design

Author: Hugo Kubinyi

Publisher: Springer Science & Business Media

Published: 2006-04-11

Total Pages: 413

ISBN-13: 0306468573

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Significant progress has been made in the study of three-dimensional quantitative structure-activity relationships (3D QSAR) since the first publication by Richard Cramer in 1988 and the first volume in the series. 3D QSAR in Drug Design. Theory, Methods and Applications, published in 1993. The aim of that early book was to contribute to the understanding and the further application of CoMFA and related approaches and to facilitate the appropriate use of these methods. Since then, hundreds of papers have appeared using the quickly developing techniques of both 3D QSAR and computational sciences to study a broad variety of biological problems. Again the editor(s) felt that the time had come to solicit reviews on published and new viewpoints to document the state of the art of 3D QSAR in its broadest definition and to provide visions of where new techniques will emerge or new appli- tions may be found. The intention is not only to highlight new ideas but also to show the shortcomings, inaccuracies, and abuses of the methods. We hope this book will enable others to separate trivial from visionary approaches and me-too methodology from in- vative techniques. These concerns guided our choice of contributors. To our delight, our call for papers elicited a great many manuscripts.


Book Synopsis 3D QSAR in Drug Design by : Hugo Kubinyi

Download or read book 3D QSAR in Drug Design written by Hugo Kubinyi and published by Springer Science & Business Media. This book was released on 2006-04-11 with total page 413 pages. Available in PDF, EPUB and Kindle. Book excerpt: Significant progress has been made in the study of three-dimensional quantitative structure-activity relationships (3D QSAR) since the first publication by Richard Cramer in 1988 and the first volume in the series. 3D QSAR in Drug Design. Theory, Methods and Applications, published in 1993. The aim of that early book was to contribute to the understanding and the further application of CoMFA and related approaches and to facilitate the appropriate use of these methods. Since then, hundreds of papers have appeared using the quickly developing techniques of both 3D QSAR and computational sciences to study a broad variety of biological problems. Again the editor(s) felt that the time had come to solicit reviews on published and new viewpoints to document the state of the art of 3D QSAR in its broadest definition and to provide visions of where new techniques will emerge or new appli- tions may be found. The intention is not only to highlight new ideas but also to show the shortcomings, inaccuracies, and abuses of the methods. We hope this book will enable others to separate trivial from visionary approaches and me-too methodology from in- vative techniques. These concerns guided our choice of contributors. To our delight, our call for papers elicited a great many manuscripts.

Computer-Aided Drug Design

Computer-Aided Drug Design

Author: Dev Bukhsh Singh

Publisher: Springer Nature

Published: 2020-10-09

Total Pages: 308

ISBN-13: 9811568154

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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.


Book Synopsis Computer-Aided Drug Design by : Dev Bukhsh Singh

Download or read book Computer-Aided Drug Design written by Dev Bukhsh Singh and published by Springer Nature. This book was released on 2020-10-09 with total page 308 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.