Search Results: drug-design-structure-and-ligand-based-approaches

Drug Design

Structure- and Ligand-Based Approaches

Author: Kenneth M. Merz, Jr,Dagmar Ringe,Charles H. Reynolds

Publisher: Cambridge University Press

ISBN: 0521887232

Category: Medical

Page: 274

View: 7561

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.

Trypanosomatid Diseases

Molecular Routes to Drug Discovery

Author: Timo Jäger,Oliver Koch,Leopold Flohé

Publisher: John Wiley & Sons

ISBN: 3527670408

Category: Medical

Page: 576

View: 7666

This is the first resource to provide researchers in academia and industry with an urgently needed update on drug intervention against trypanosomatides. As such, it covers every aspect of the topic from basic research findings, via current treatments to translational approaches in drug development and includes both human and livestock diseases. The outstanding editor and contributor team reads like a Who?s Who of the field, thus guaranteeing the outstanding quality of this ready reference.

Computational and Structural Approaches to Drug Discovery

Ligand-protein Interactions

Author: Robert M. Stroud,Janet Finer-Moore

Publisher: Royal Society of Chemistry

ISBN: 0854043659

Category: Medical

Page: 382

View: 1643

This insightful book represents the experience and understanding of the global experts in the field and spotlights both the structural and medicinal chemistry aspects of drug design. The need to 'encode' the physiological factors of pharmacology, a key area, is explored.

Applied Chemoinformatics

Achievements and Future Opportunities

Author: Thomas Engel,Johann Gasteiger

Publisher: John Wiley & Sons

ISBN: 3527806520

Category: Science

Page: 416

View: 7348

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.

Structure-based Ligand Design

Author: Klaus Gubernator,Hans-Joachim Böhm

Publisher: John Wiley & Sons

ISBN: 3527612165

Category: Science

Page: 167

View: 7882

Most drugs bind to a clearly defined macromolecular target that is complementary in terms of structure and chemistry. This observation is the basic paradigm of structure-based ligand design. Although this method first emerged in the 1980s, it has already become a powerful tool for pharmaceutical research. Much has been learned, however, since the first attempts to discover drugs on the basis of available biochemical and structural data. Nowadays, structure-based ligand design is an established method for creating drugs with new structural features, for modifying binding activities and pharmacokinetic properties, and for elucidating binding modes and structure-activity relationships. This volume presents the underlying principles of the approach and highlights real-life applications such as the discovery of HIV-protease inhibitors. It shows that structure-based ligand design has many advantages over other more traditional approaches to designing new drugs, providing it is employed properly and with a thorough knowledge of the pitfalls to avoid. The straightforward presentation and extensive list of references to the original literature as well as numerous color figures illustrating structural relationships make this volume an indispensable tool for every scientist working in the area of drug discovery.

Drug Design Strategies

Computational Techniques and Applications

Author: Lee Banting,Tim Clark,David E. Thurston

Publisher: Royal Society of Chemistry

ISBN: 1849731675

Category: Medical

Page: 239

View: 4112

This book, aimed at academics, industrialists and post-graduates, documents the latest research into computer aided drug design.

Quantitative Structure-Activity Relationships in Drug Design, Predictive Toxicology, and Risk Assessment

Author: Roy, Kunal

Publisher: IGI Global

ISBN: 1466681373

Category: Technology & Engineering

Page: 727

View: 3498

Quantitative structure-activity relationships (QSARs) represent predictive models derived from the application of statistical tools correlating biological activity or other properties of chemicals with descriptors representative of molecular structure and/or property. Quantitative Structure-Activity Relationships in Drug Design, Predictive Toxicology, and Risk Assessment discusses recent advancements in the field of QSARs with special reference to their application in drug development, predictive toxicology, and chemical risk analysis. Focusing on emerging research in the field, this book is an ideal reference source for industry professionals, students, and academicians in the fields of medicinal chemistry and toxicology.

Computational Chemistry Methods in Structural Biology

Author: N.A

Publisher: Academic Press

ISBN: 0123864860

Category: Science

Page: 360

View: 5289

Published continuously since 1944, the Advances in Protein Chemistry and Structural Biology serial has been a continuous, essential resource for protein chemists. Covering reviews of methodology and research in all aspects of protein chemistry, including purification/expression, proteomics, modeling and structural determination and design, each volume brings forth new information about protocols and analysis of proteins while presenting the most recent findings from leading experts in a broad range of protein-related topics. This volume features articles on Computational Chemistry methods in Structural Biology. Essential resource for protein chemists This volume features articles on Computational Chemistry methods in Structural Biology

Bioinformatics Techniques for Drug Discovery

Applications for Complex Diseases

Author: Aman Chandra Kaushik,Ajay Kumar,Shiv Bharadwaj,Ravi Chaudhary,Shakti Sahi

Publisher: Springer

ISBN: 3319757326

Category: Computers

Page: 57

View: 1511

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.

Structure-based Design of Drugs and Other Bioactive Molecules

Tools and Strategies

Author: Arun K. Ghosh,Sandra Gemma

Publisher: John Wiley & Sons

ISBN: 3527665234

Category: Medical

Page: 474

View: 472

Drug design is a complex, challenging and innovative research area. Structure-based molecular design has transformed the drug discovery approach in modern medicine. Traditionally, focus has been placed on computational, structural or synthetic methods only in isolation. This one-of-akind guide integrates all three skill sets for a complete picture of contemporary structure-based design. This practical approach provides the tools to develop a high-affinity ligand with drug-like properties for a given drug target for which a high-resolution structure exists. The authors use numerous examples of recently developed drugs to present "best practice" methods in structurebased drug design with both newcomers and practicing researchers in mind. By way of a carefully balanced mix of theoretical background and case studies from medicinal chemistry applications, readers will quickly and efficiently master the basic skills of successful drug design. This book is aimed at new and active medicinal chemists, biochemists, pharmacologists, natural product chemists and those working in drug discovery in the pharmaceutical industry. It is highly recommended as a desk reference to guide students in medicinal and chemical sciences as well as to aid researchers engaged in drug design today.

Structure-Based Drug Design

Experimental and Computational Approaches

Author: P.W. Codding

Publisher: Springer Science & Business Media

ISBN: 9401590281

Category: Science

Page: 290

View: 8857

Structure-Based Drug Design brings together scientists working on different aspects of the subject, demonstrating the necessary collaboration and interdisciplinary approach to this complex area. The focus is on X-ray crystallographic and computational approaches. The general aspects of these approaches are introduced in the first six articles. The remaining articles provide examples of the application of X-ray crystallography, molecular modelling, molecular dynamics, QSAR, database analysis, and homology modelling. The papers cover a wealth of interesting problems in the design of new and enhanced pharmaceuticals.

Chemoinformatics Approaches to Virtual Screening

Author: Alexandre Varnek,Alex Tropsha

Publisher: Royal Society of Chemistry

ISBN: 0854041443

Category: Science

Page: 338

View: 3116

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.

QSAR and Drug Design: New Developments and Applications

Author: H. Timmerman

Publisher: Elsevier

ISBN: 9780080545004

Category: Science

Page: 490

View: 4183

Based on topics presented at the Annual Japanese (Quantitative) Structure-Activity Relationship Symposium and the Biennial China-Japan Drug Design and Development conference, the topics in this volume cover almost every procedure and subdiscipline in the SAR discipline. They are categorized in three sections. Section one includes topics illustrating newer methodologies relating to ligand-receptor, molecular graphics and receptor modelling as well as the three-dimensional (Q)SAR examples with the active analogue approach and the comparative molecular field analysis. In section 2 the hydrophobicity parameters, log P (1-octanol/water) for compound series of medicinal-chemical interest are analysed physico-organic chemically. Section 3 contains the examples based on the traditional Hansch QSAR approach. A variety of methodologies and procedures are presented in this single volume, along with their methodological philosophies.

Chemical Drug Design

Author: Girish Kumar Gupta,Vinod Kumar

Publisher: Walter de Gruyter GmbH & Co KG

ISBN: 311036882X

Category: Science

Page: 297

View: 2349

Chemical Drug Design provides a compact overview on recent advances in this rapidly developing field. With contributions on in silico drug design, natural product based compounds, as well as on ligand- and structure-based approaches, the authors present innovative methods and techniques for identifying and synthetically designing novel drugs.

Genetic Engineering News


Author: N.A

Publisher: N.A


Category: Genetic engineering

Page: N.A

View: 7786

Structure-based Drug Discovery

An Overview

Author: R. E. Hubbard

Publisher: Royal Society of Chemistry

ISBN: 0854043519

Category: Medical

Page: 261

View: 6492

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.

Frontiers in Drug Design and Discovery

Author: Atta-ur- Rahman

Publisher: Bentham Science Publishers

ISBN: 160805201X

Category: Medical

Page: 634

View: 4018

"Frontiers in Drug Design and Discovery" is an Ebook series devoted to publishing the latest and the most important advances in drug design and discovery. Eminent scientists write contributions on all areas of rational drug design and drug discovery including medicinal chemistry, in-silico drug design, combinatorial chemistry, high-throughput screening, drug targets, and structure-activity relationships. the Ebook series should prove to be of interest to all the pharmaceutical scientists involved in research in drug design and discovery. Each volume is devoted to the major advances in drug design and discovery. the Ebook series is essential reading to all scientists involved in drug design and discovery who wish to keep abreast of rapid and important developments in the field.

Pharmacophores and Pharmacophore Searches

Author: Thierry Langer,Rémy D. Hoffmann

Publisher: John Wiley & Sons

ISBN: 3527608729

Category: Science

Page: 395

View: 6114

This handbook is the first to address the practical aspects of this novel method. It provides a complete overview of the field and progresses from general considerations to real life scenarios in drug discovery research. Starting with an introductory historical overview, the authors move on to discuss ligand-based approaches, including 3D pharmacophores and 4D QSAR, as well as the concept and application of pseudoreceptors. The next section on structure-based approaches includes pharmcophores from ligand-protein complexes, FLIP and 3D protein-ligand binding interactions. The whole is rounded off with a complete section devoted to applications and examples, including modeling of ADME properties. With its critical evaluation of pharmacophore-based strategies, this book represents a valuable aid for project leaders and decision-makers in the pharmaceutical industry, as well as pharmacologists, and medicinal and chemists.

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

Author: Dastmalchi, Siavoush

Publisher: IGI Global

ISBN: 1522501169

Category: Medical

Page: 456

View: 4821

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.

Fragment Based Drug Design

Tools, Practical Approaches, and Examples

Author: N.A

Publisher: Academic Press

ISBN: 0123812755

Category: Medical

Page: 645

View: 1928

There are numerous excellent reviews on fragment-based drug discovery (FBDD), but there are to date no hand-holding guides or protocols with which one can embark on this orthogonal approach to complement traditional high throughput screening methodologies. This Methods in Enzymology volume offers the tools, practical approaches, and hit-to-lead examples on how to conduct FBDD screens. The chapters in this volume cover methods that have proven to be successful in generating leads from fragments, including chapters on how to apply computational techniques, nuclear magnetic resonance, surface plasma resonance, thermal shift and binding assays, protein crystallography, and medicinal chemistry in FBDD. Also elaborated by experienced researchers in FBDD are sample preparations of fragments, proteins, and GPCR as well as examples of how to generate leads from hits. Offers the tools, practical approaches, and hit-to-lead examples on how to conduct FBDD screens The chapters in this volume cover methods that have proven to be successful in generating leads from fragments, including chapters on how to apply computational techniques, nuclear magnetic resonance, surface plasma resonance, thermal shift and binding assays, protein crystallography, and medicinal chemistry in FBDD

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