Search Results for virtual-screening-in-drug-discovery

Virtual screening can reduce costs and increase hit rates for lead discovery by eliminating the need for robotics, reagent acquisition or production, and compound storage facilities.

Author: Juan Alvarez

Publisher: CRC Press

ISBN: 9781420028775

Category: Medical

Page: 496

View: 803

Virtual screening can reduce costs and increase hit rates for lead discovery by eliminating the need for robotics, reagent acquisition or production, and compound storage facilities. The increased robustness of computational algorithms and scoring functions, the availability of affordable computational power, and the potential for timely structural determination of target molecules, have provided new opportunities for virtual screening, and made it more practical. Why then, isn’t everyone using virtual screening? Examining the scope and limitations of this method, Virtual Screening in Drug Discovery explores the algorithms involved and how to actually use them. Part I offers perspectives on both ligand-based and docking-based virtual screens. The authors of these chapters frame many of the challenges currently facing the field. Part II considers the choice of compounds that are best suited as drug leads. Part III discusses ligand-based approaches, including descriptor-based similarity, traditional pharmacophore searching, and similarity based 3D-pharmacophore fingerprints. The final two sections are devoted to molecular docking. Part IV outlines some important and practical considerations relating to the energetics of protein-ligand binding and target-site topography, whereas specific docking algorithms and strategies are discussed in Part V. Notwithstanding this list of subjects, the book does not overwhelm you with more information than you need—many of the strategies outlined will transcend the specifics of any given method. Nor does the book purport to offer single best ways to use the programs. What it does is provide a snapshot of virtual screening that gives you easy access to strategies and techniques for lead discovery. Daniel E. Levy, editor of the Drug Discovery Series, is the founder of DEL BioPharma, a consulting service for drug discovery programs. He also maintains a blog that explores organic chemistry.
2005-03-24 By Juan Alvarez

Unique in its focus on the end user, this is a real "how to" book that does not presuppose prior experience in virtual screening or a background in computational chemistry.

Author: Christoph Sotriffer

Publisher: John Wiley & Sons

ISBN: 9783527633340

Category: Medical

Page: 550

View: 923

Drug discovery is all about finding small molecules that interact in a desired way with larger molecules, namely proteins and other macromolecules in the human body. If the three-dimensional structures of both the small and large molecule are known, their interaction can be tested by computer simulation with a reasonable degree of accuracy. Alternatively, if active ligands are already available, molecular similarity searches can be used to find new molecules. This virtual screening can even be applied to compounds that have yet to be synthesized, as opposed to "real" screening that requires cost- and labor-intensive laboratory testing with previously synthesized drug compounds. Unique in its focus on the end user, this is a real "how to" book that does not presuppose prior experience in virtual screening or a background in computational chemistry. It is both a desktop reference and practical guide to virtual screening applications in drug discovery, offering a comprehensive and up-to-date overview. Clearly divided into four major sections, the first provides a detailed description of the methods required for and applied in virtual screening, while the second discusses the most important challenges in order to improve the impact and success of this technique. The third and fourth, practical parts contain practical guidelines and several case studies covering the most important scenarios for new drug discovery, accompanied by general guidelines for the entire workflow of virtual screening studies. Throughout the text, medicinal chemists from academia, as well as from large and small pharmaceutical companies report on their experience and pass on priceless practical advice on how to make best use of these powerful methods.
2011-03-31 By Christoph Sotriffer

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.

Author: Mohini Gore

Publisher: Humana

ISBN: 1493992767

Category: Medical

Page: 488

View: 549

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.
2019-04-12 By Mohini Gore

Good A. Structure-based virtual screening protocols. Curr Opin Drug Discov Dev
2001;4:301—7. Langer T, Hoffmann RD. Virtual screening: an effective tool for
lead structure discovery? Curr Pharm Des 2001;7:509—27. Schneider G, Bdhm ...

Author: Sean Ekins

Publisher: John Wiley & Sons

ISBN: 9780470037225

Category: Medical

Page: 805

View: 823

A unique, holistic approach covering all functions and phases of pharmaceutical research and development While there are a number of texts dedicated to individual aspects of pharmaceutical research and development, this unique contributed work takes a holistic and integrative approach to the use of computers in all phases of drug discovery, development, and marketing. It explains how applications are used at various stages, including bioinformatics, data mining, predicting human response to drugs, and high-throughput screening. By providing a comprehensive view, the book offers readers a unique framework and systems perspective from which they can devise strategies to thoroughly exploit the use of computers in their organizations during all phases of the discovery and development process. Chapters are organized into the following sections: * Computers in pharmaceutical research and development: a general overview * Understanding diseases: mining complex systems for knowledge * Scientific information handling and enhancing productivity * Computers in drug discovery * Computers in preclinical development * Computers in development decision making, economics, and market analysis * Computers in clinical development * Future applications and future development Each chapter is written by one or more leading experts in the field and carefully edited to ensure a consistent structure and approach throughout the book. Figures are used extensively to illustrate complex concepts and multifaceted processes. References are provided in each chapter to enable readers to continue investigating a particular topic in depth. Finally, tables of software resources are provided in many of the chapters. This is essential reading for IT professionals and scientists in the pharmaceutical industry as well as researchers involved in informatics and ADMET, drug discovery, and technology development. The book's cross-functional, all-phases approach provides a unique opportunity for a holistic analysis and assessment of computer applications in pharmaceutics.
2006-07-11 By Sean Ekins

Villoutreix, B.O.; Eudes, R.; Miteva, M.A. Structure-based virtual ligand screening:
Recent success stories. Combinatorial Chemistry & High Throughput Screening
2009, 12, 1000-1016. Kuntz, I.D. Structure-based strategies for drug design and ...

Author: Maria A. Miteva

Publisher: Bentham Science Publishers

ISBN: 9781608051427

Category: Science

Page: 193

View: 780

Computer-aided drug design and in silico screening have contributed to the discovery of several compounds that have either reached the market or entered clinical trials. In silico Lead Discovery is a compilation of the efforts of several experts on bioinf

VIRTUAL SCREENING Jürgen Bajorath B-IT, International Center for Information
Technology Rheinische Friedrich–Wilhelms–University Bonn Bonn, Germany 3.1

Author: Shayne Cox Gad

Publisher: John Wiley & Sons

ISBN: 9780471728771

Category: Science

Page: 1496

View: 365

The Drug Discovery Handbook gives professionals a tool tofacilitate drug discovery by bringing together, for the first timein one resource, a compendium of methods and techniques that needto be considered when developing new drugs. This comprehensive, practical guide presents an explanation of thelatest techniques and methods in drug discovery, including: Genomics, proteomics, high-throughput screening, and systemsbiology Summaries of how these techniques and methods are used todiscover new central nervous system agents, antiviral agents,respiratory drugs, oncology drugs, and more Specific approaches to drug discovery, including problems thatare encountered, solutions to these problems, and limitations ofvarious methods and techniques The thorough coverage and practical, scientifically validproblem-solving approach of Drug Discovery Handbook will serve asan invaluable aid in the complex task of developing new drugs.
2005-07-08 By Shayne Cox Gad

Virtual screening of drugs: Score functions, docking, and drug design. Current
Computer-Aided Drug Designs 4, 265–272. ... Structure-based virtual screening
of chemical libraries for drug discovery. Current Opinion in Chemical Biology 10(
3), ...


Publisher: Elsevier

ISBN: 9780128114322

Category: Medical

Page: 3284

View: 777

Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics combines elements of computer science, information technology, mathematics, statistics and biotechnology, providing the methodology and in silico solutions to mine biological data and processes. The book covers Theory, Topics and Applications, with a special focus on Integrative –omics and Systems Biology. The theoretical, methodological underpinnings of BCB, including phylogeny are covered, as are more current areas of focus, such as translational bioinformatics, cheminformatics, and environmental informatics. Finally, Applications provide guidance for commonly asked questions. This major reference work spans basic and cutting-edge methodologies authored by leaders in the field, providing an invaluable resource for students, scientists, professionals in research institutes, and a broad swath of researchers in biotechnology and the biomedical and pharmaceutical industries. Brings together information from computer science, information technology, mathematics, statistics and biotechnology Written and reviewed by leading experts in the field, providing a unique and authoritative resource Focuses on the main theoretical and methodological concepts before expanding on specific topics and applications Includes interactive images, multimedia tools and crosslinking to further resources and databases
2018-08-21 By

Development. and. Application. of. Virtual. Screening. in. Drug. Discovery: An.
Overview. Tingjun. Hou. and. Xiaojie. Xu*. College of Chemistry and Molecular
Engineering, Peking University, Beijing 100871, China Abstract: Virtual
screening, ...

Author: Atta-ur- Rahman

Publisher: Bentham Science Publishers

ISBN: 9781608052066

Category: Medical

Page: 715

View: 831

""Frontiers in Medicinal Chemistry" is an Ebook series devoted to the review of areas of important topical interest to medicinal chemists and others in allied disciplines. "Frontiers in Medicinal Chemistry" covers all the areas of medicinal chemistry, incl"
2010-12-10 By Atta-ur- Rahman

Methods for compound selection focused on hits and application in drug
discovery. Journal of Molecular Graphics and ... Waszkowycz B. Towards
improving compound selection in structurebased virtual screening. Drug
Discovery Today 2008 ...

Author: Raymond G Hill

Publisher: Elsevier Health Sciences

ISBN: 9780702053160

Category: Medical

Page: 368

View: 890

The modern pharmacopeia has enormous power to alleviate disease, and owes its existence almost entirely to the work of the pharmaceutical industry. This book provides an introduction to the way the industry goes about the discovery and development of new drugs. The first part gives a brief historical account from its origins in the mediaeval apothecaries’ trade, and discusses the changing understanding of what we mean by disease, and what therapy aims to achieve, as well as summarising case histories of the discovery and development of some important drugs. The second part focuses on the science and technology involved in the discovery process: the stages by which a promising new chemical entity is identified, from the starting point of a medical need and an idea for addressing it. A chapter on biopharmaceuticals, whose discovery and development tend to follow routes somewhat different from synthetic compounds, is included here, as well as accounts of patent issues that arise in the discovery phase, and a chapter on research management in this environment. The third section of the book deals with drug development: the work that has to be undertaken to turn the drug candidate that emerges from the discovery process into a product on the market. The definitive introduction to how a pharmaceutical company goes about its business of discovering and developing drugs. The second edition has a new editor: Professor Raymond Hill ● non-executive director of Addex Pharmaceuticals, Covagen and of Orexo AB ● Visiting Industrial Professor of Pharmacology in the University of Bristol ● Visiting Professor in the School of Medical and Health Sciences at the University of Surrey ● Visiting Professor in Physiology and Pharmacology at the University of Strathclyde ● President and Chair of the Council of the British Pharmacological Society ● member of the Nuffield Council on Bioethics and the Advisory Council on Misuse of Drugs. New to this edition: Completely rewritten chapter on The Role of Medicinal Chemistry in the Drug Discovery Process. New topic - DMPK Optimization Strategy in drug discovery. New chapter on Scaffolds: Small globular proteins as antibody substitutes. Totally updated chapters on Intellectual Property and Marketing 50 new illustrations in full colour Features Accessible, general guide to pharmaceutical research and development. Examines the interfaces between cost and social benefit, quality control and mass production, regulatory bodies, patent management, and all interdisciplinary intersections essential to effective drug development. Written by a strong team of scientists with long experience in the pharmaceutical industry. Solid overview of all the steps from lab bench to market in an easy-to-understand way which will be accessible to non-specialists. From customer reviews of the previous edition: ‘... it will have everything you need to know on this module. Deeply referenced and, thus, deeply reliable. Highly Commended in the medicine category of the BMA 2006 medical book competition Winner of the Royal Society of Medicine Library Prize for Medical Book of the Year
2012-07-20 By Raymond G Hill

A collection of methods to determine and analyse the 3-D structure of biomolecules. These methods have been enhanced to improve the speed and quality of drug discovery.

Author: R. E. Hubbard

Publisher: Royal Society of Chemistry

ISBN: 9780854043514

Category: Medical

Page: 261

View: 477

A collection of methods to determine and analyse the 3-D structure of biomolecules. These methods have been enhanced to improve the speed and quality of drug discovery.
2006-01-01 By R. E. Hubbard

In Bioinformatics and Drug Discovery, a panel of researchers from academic and pharmaceutical laboratories describes readily reproducible bioinformatic methods to advance the drug discovery process from gene identification to protein ...

Author: Richard S. Larson

Publisher: Humana Press

ISBN: 1617375098

Category: Medical

Page: 444

View: 610

A collection of readily reproducible bioinformatic methods to advance the drug discovery process from gene identification to protein modeling to the identification of specific drug candidates. The authors demonstrate these techniques, including microarray analysis, the analysis of genes as potential drug targets, virtual screening and in silico protein design, and cheminformatics, in a variety of practical situations. Because these technologies are still emergent, each chapter contains an extended introduction that explains the theory and application of the technology and techniques described.
2010-10-28 By Richard S. Larson

Why then is Virtual Screening such an important area of research? The answer to
this question is illustrated by Figure 1. There are ~ 107 compounds registered in
Chemical Abstracts, around 104 compounds in the World Drug Index,2 and, ...

Author: Royal Society of Chemistry (Great Britain)

Publisher: Royal Society of Chemistry

ISBN: 0854048162

Category: Medical

Page: 192

View: 766

Providing details of state-of-the-art research, Drug Design: Cutting Edge Approaches will be invaluable to all drug discovery scientists.

Proceedings of the Workshop 'New Approaches in Drug Design and Discovery',
special topic 'Virtual Screening', Schloß Rauischholzhausen, Germany, March 15
–18, 1999 Gerhard Klebe. at in cases where a systematic approach is ...

Author: Gerhard Klebe

Publisher: Springer Science & Business Media

ISBN: 9780306468834

Category: Medical

Page: 295

View: 114

In the next couple of years the human genome will be fully sequenced. This will provide us with the sequence and overall function of all human genes as well as the complete genome for many micro-organisms. Subsequently it is hoped, by means of powerful bioinformatic tools, to determine the gene variants that contribute to various multifactorial diseases and genes that exist in certain infectious agents but not humans. As a consequence, this will allow us to define the most appropriate levels for drug intervention. It can be expected that the number of potential drug targets will increase, possibly by a factor of 10 or more. Nevertheless, sequencing the human genome or, for that matter, the genome of other species will only be the starting point for the understanding of their biological function. Structural genomics is a likely follow-up, combined with new techniques to validate the therapeutic relevance of such newly discovered targets. Accordingly, it can be expected that in the near future we will witness a substantial increase in novel putative targets for drugs. To address these new targets effectively, we require new approaches and innovative tools. At present, two alternative, yet complementary, techniques are employed: experimental high-throughput screening (HTS) of large compound libraries, increasingly provided by combinatorial chemistry, and computational methods for virtual screening and de novo design. As kind of status report on the maturity of virtual screening as a technique in drug design, the first workshop on new approaches in drug design and discovery was held in March 1999, at Schloß Rauischholzhausen, near Marburg in Germany. More than 80 scientists gathered and discussed their experience with the different techniques. The speakers were invited to summarize their contributions together with their impressions on the present applicability of their approach. Several of the speakers followed this request which is summarized in this publication.
2007-05-08 By Gerhard Klebe

One of the principal architects of lead generation as a separate phase within the
pharmaceutical industry was Bill Michne ... in silico or “virtualscreening plays an
increasingly important role at this early stage of the drug discovery process.

Author: Zoran Rankovic

Publisher: John Wiley & Sons

ISBN: 0470584165

Category: Medical

Page: 308

View: 851

An integrated overview of modern approaches to lead discovery Lead generation is increasingly seen as a distinct and success-determining phase of the drug discovery process. Over recent years, there have been major advances in the understanding of what constitutes a good lead compound and how to improve the chances of finding such a compound. Written by leading scientists and established opinion leaders from industry and academia, this book provides an authoritative overview of the field, as well as the theory, practice, and scope, of the principal Lead Generation Approaches in Drug Discovery, including: The evolution of the lead discovery process, key concepts, current challenges, and future directions Strategies and technologies driving the high-throughput screening (HTS) approach to lead discovery, including the shifting paradigms in the design of compound collections and best practice in the hit confirmation process Knowledge-based in silico or "virtual" screening Theory and practice of the fragment-based approach to lead discovery The opportunities and challenges presented by multi-target drug discovery (MTDD) De novo design of lead compounds and new approaches to estimating the synthetic accessibility of de novo–designed molecules The impact of natural products on drug discovery, and potential of natural product–like compounds for exploring regions of biologically relevant chemical space Using early screening of hits and leads for metabolic, pharmacokinetic, and toxicological liabilities to reduce attrition during the later phases of drug discovery The utility of parallel synthesis and purification in lead discovery With each topic supported by numerous case studies, this is indispensable reading for researchers in industry and academia who wish to keep up to date with the latest strategies and approaches in drug discovery.
2010-04-07 By Zoran Rankovic

Strategies for Drug Discovery and Development George C. Prendergast ... Drug
Discovery Today 5 , 145-156 ( 2000 ) . Liu , Y. , Kati ... Toledo - Sherman , L. M. ,
and Chen , D. High - throughput virtual screening for drug discovery in parallel .

Author: George C. Prendergast

Publisher: John Wiley & Sons

ISBN: 0471432024

Category: Science

Page: 351

View: 850

Molecular Cancer Therapeutics covers state-of-the-art strategies to identify and develop cancer drug target molecules and lead inhibitors for clinical testing. It provides a thorough treatment of drug target discovery, validation, and development. The introductory chapters provide an overview of pathways to discovery and development of molecular cancer therapeutics. Subsequent chapters progress from initial stages of drug target discovery to drug discovery, development, and testing in preclinical and clinical models. Topics include drug lead screening, drug-to-lead development, proof-of-concept studies, medicinal chemistry issues, intellectual property concerns, and clinical development. This invaluable reference promotes understanding of steps involved in developing drug leads for industrial partnering and development. It provides an overview of the strategies for discovery and validation of drug target molecules, and discusses cell- and molecule-based drug screening strategies, as well as mouse models for cancer. Coverage also includes how to refine drug leads for suitability in clinical testing, the special issues of clinical testing of molecular-targeted drugs, and intellectual property concerns.
2004-04-02 By George C. Prendergast

This handbook is unique in bringing together the various efforts in the field of virtual screening to provide the necessary methodological framework for more effective research.

Author: Hans-Joachim Böhm

Publisher: John Wiley & Sons

ISBN: 9783527613090

Category: Science

Page: 325

View: 591

Recent progress in high-throughput screening, combinatorial chemistry and molecular biology has radically changed the approach to drug discovery in the pharmaceutical industry. New challenges in synthesis result in new analytical methods. At present, typically 100,000 to one million molecules have to be tested within a short period and, therefore, highly effective screening methods are necessary for today's researchers - preparing and characterizing one compound after another belongs to the past. Intelligent, computer-based search agents are needed and "virtual screening" provides solutions to many problems. Such screening comprises innovative computational techniques designed to turn raw data into valuable chemical information and to assist in extracting the relevant molecular features. This handbook is unique in bringing together the various efforts in the field of virtual screening to provide the necessary methodological framework for more effective research. Leading experts give a thorough introduction to the state of the art along with a critical assessment of both successful applications and drawbacks. The information collated here will be indispensable for experienced scientists, as well as novices, working in medicinal chemistry and related disciplines.
2008-11-21 By Hans-Joachim Böhm

the. Discovery. of. Novel. Drugs. Mahmud Tareq Hassan Khan and Ingebrigt
Sylte Abstract There have been extensive ... review, some of the recent methods
discussed briefly concerning their aspects of docking, virtual screening and
virtual ...

Author: Bilge Sener

Publisher: Springer Science & Business Media

ISBN: 9781402069550

Category: Science

Page: 428

View: 143

This book includes 49 chapters presented as plenary , invited lectures and posters at the conference. Six plenary lectures have published in an issue of Pure and Applied Chemistry, Vol. 79, No. 12, 2007; the titles of these presentations are given as an Annex at the end of the book. I thank all contrib utors for the preparation of their presentations. It is sad to report that Professor Hitoshi Ohtaki, one of the founders of the Eurasia conferences and contributors passed away on November 5, 2006. Professor Ohtaki enthusiastically promoted international cooperation and took it upon himself to p- licize Japanese science to the wider world. His contribution in this book will serve as a memorable contribution to that goal. He will be missed by all of us. This book is dedicated to his memory. Professor Dr . Bilge S ̧ ener Editor Memorial Tribute to Professor Dr. Hitoshi Ohtaki Curriculum Vitae of Hitoshi Ohtaki Date of Birth September 16, 1932 Place of Birth T ok yo, Japan Date of Decease November 5, 2006 (at the age of 74) Addr ess 3-9-406 Namiki-2-chome, Kanazawa-ku, Yokohama, Japan Institution Chair Professor of The Research Organization of Science and Engineering, Ritsumeikan University Guest Professor of Yokohama City University Education Bachelor of Science, Nagoya University, 1955 Master of Science, Nagoya University, 1957 Doctor of Science, Nagoya University, 1961 ix x Memorial Tribute to Professor Dr.
2008-11-23 By Bilge Sener

Virtual. Screening. in. Drug. Discovery. CHRISTIAN LAGGNER,a GERHARD
LANGERa, b a Department of Pharmaceutical Chemistry, Faculty of Chemistry
and ...

Author: Alexandre Varnek

Publisher: Royal Society of Chemistry

ISBN: 9780854041442

Category: Science

Page: 338

View: 233

Chemoinformatics is broadly a scientific discipline encompassing the design, creation, organization, management, retrieval, analysis, dissemination, visualization and use of chemical information. It is distinct from other computational molecular modeling approaches in that it uses unique representations of chemical structures in the form of multiple chemical descriptors; has its own metrics for defining similarity and diversity of chemical compound libraries; and applies a wide array of statistical, data mining and machine learning techniques to very large collections of chemical compounds in order to establish robust relationships between chemical structure and its physical or biological properties. Chemoinformatics addresses a broad range of problems in chemistry and biology; however, the most commonly known applications of chemoinformatics approaches have been arguably in the area of drug discovery where chemoinformatics tools have played a central role in the analysis and interpretation of structure-property data collected by the means of modern high throughput screening. Early stages in modern drug discovery often involved screening small molecules for their effects on a selected protein target or a model of a biological pathway. In the past fifteen years, innovative technologies that enable rapid synthesis and high throughput screening of large libraries of compounds have been adopted in almost all major pharmaceutical and biotech companies. As a result, there has been a huge increase in the number of compounds available on a routine basis to quickly screen for novel drug candidates against new targets/pathways. In contrast, such technologies have rarely become available to the academic research community, thus limiting its ability to conduct large scale chemical genetics or chemical genomics research. However, the landscape of publicly available experimental data collection methods for chemoinformatics has changed dramatically in very recent years. The term "virtual screening" is commonly associated with methodologies that rely on the explicit knowledge of three-dimensional structure of the target protein to identify potential bioactive compounds. Traditional docking protocols and scoring functions rely on explicitly defined three dimensional coordinates and standard definitions of atom types of both receptors and ligands. Albeit reasonably accurate in many cases, conventional structure based virtual screening approaches are relatively computationally inefficient, which has precluded them from screening really large compound collections. Significant progress has been achieved over many years of research in developing many structure based virtual screening approaches. This book is the first monograph that summarizes innovative applications of efficient chemoinformatics approaches towards the goal of screening large chemical libraries. The focus on virtual screening expands chemoinformatics beyond its traditional boundaries as a synthetic and data-analytical area of research towards its recognition as a predictive and decision support scientific discipline. The approaches discussed by the contributors to the monograph rely on chemoinformatics concepts such as: -representation of molecules using multiple descriptors of chemical structures -advanced chemical similarity calculations in multidimensional descriptor spaces -the use of advanced machine learning and data mining approaches for building quantitative and predictive structure activity models -the use of chemoinformatics methodologies for the analysis of drug-likeness and property prediction -the emerging trend on combining chemoinformatics and bioinformatics concepts in structure based drug discovery The chapters of the book are organized in a logical flow that a typical chemoinformatics project would follow - from structure representation and comparison to data analysis and model building to applications of structure-property relationship models for hit identification and chemical library design. It opens with the overview of modern methods of compounds library design, followed by a chapter devoted to molecular similarity analysis. Four sections describe virtual screening based on the using of molecular fragments, 2D pharmacophores and 3D pharmacophores. Application of fuzzy pharmacophores for libraries design is the subject of the next chapter followed by a chapter dealing with QSAR studies based on local molecular parameters. Probabilistic approaches based on 2D descriptors in assessment of biological activities are also described with an overview of the modern methods and software for ADME prediction. The book ends with a chapter describing the new approach of coding the receptor binding sites and their respective ligands in multidimensional chemical descriptor space that affords an interesting and efficient alternative to traditional docking and screening techniques. Ligand-based approaches, which are in the focus of this work, are more computationally efficient compared to structure-based virtual screening and there are very few books related to modern developments in this field. The focus on extending the experiences accumulated in traditional areas of chemoinformatics research such as Quantitative Structure Activity Relationships (QSAR) or chemical similarity searching towards virtual screening make the theme of this monograph essential reading for researchers in the area of computer-aided drug discovery. However, due to its generic data-analytical focus there will be a growing application of chemoinformatics approaches in multiple areas of chemical and biological research such as synthesis planning, nanotechnology, proteomics, physical and analytical chemistry and chemical genomics.

Then, M. Rarey et al. review ''Algorithmic Engines in Virtual Screening'' and D.
Horvath et al. review the ''Strengths and Limitations of Pharmacophore-Based
Virtual Screening''. The next section is dedicated to Hit and Lead Discovery with ...

Author: Tudor I. Oprea

Publisher: John Wiley & Sons

ISBN: 9783527604203

Category: Science

Page: 515

View: 449

This handbook provides the first-ever inside view of today's integrated approach to rational drug design. Chemoinformatics experts from large pharmaceutical companies, as well as from chemoinformatics service providers and from academia demonstrate what can be achieved today by harnessing the power of computational methods for the drug discovery process. With the user rather than the developer of chemoinformatics software in mind, this book describes the successful application of computational tools to real-life problems and presents solution strategies to commonly encountered problems. It shows how almost every step of the drug discovery pipeline can be optimized and accelerated by using chemoinformatics tools -- from the management of compound databases to targeted combinatorial synthesis, virtual screening and efficient hit-to-lead transition. An invaluable resource for drug developers and medicinal chemists in academia and industry.
2006-03-06 By Tudor I. Oprea

[3, 4] The same problem exists with virtual screening and scoring functions. A
universal scoring function for bound ligands remains a Fragment-Based Drug
Discovery: A Practical Approach Edited by Edward R. Zartler and Michael J.
Shapiro c ...

Author: Edward R. Zartler

Publisher: John Wiley & Sons

ISBN: 9780470721568

Category: Science

Page: 296

View: 864

Fragment-based drug discovery (FBDD) is a new paradigm in drug discovery that utilizes very small molecules - fragments of larger molecules. It is a faster, cheaper, smarter way to do drug discovery, as shown by the number of pharmaceutical companies that have embraced this approach and the biotechnology companies who use fragments as their sole source of drug discovery. Fragment-Based Drug Discovery: A Practical Approach is a guide to the techniques and practice of using fragments in drug screening. The emphasis is on practical guidance, with procedures, case studies, practical tips, and contributions from industry. Topics covered include: an introduction to fragment based drug discovery, why using fragments is a more efficient process than predominant models, and what it means to have a successful FBDD effort. setting up an FBDD project library building and production NMR in fragment screening and follow up application of protein-ligand NOE matching to the rapid evaluation of fragment binding poses target immobilized NMR screening: validation and extension to membrane proteins in situ fragment-based medicinal chemistry: screening by mass spectrometry computational approaches to fragment and substructure discovery and evaluation virtual fragment scanning: current trends, applications and web based tools fragment-based lead discovery using covalent capture methods case study from industry: the identification of high affinity beta-secretase inhibitors using fragment-based lead generation With contributions from industry experts who have successfully set up an industrial fragment-based research program, Fragment-Based Drug Discovery: A Practical Approach offers essential advice to anyone embarking on drug discovery using fragments and those looking for a new approach to screening for drugs.
2008-11-20 By Edward R. Zartler

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