emerging alternatives in fragment based in silico design

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Frontiers in Drug Design and Discovery
Author : Atta-ur- Rahman,Gary W. Caldwell, M. Iqbal Choudhary,Mark R. Player
Publisher : Bentham Science Publishers
Release Date : 2010-12-13
ISBN 10 : 160805201X
Pages : 644 pages

"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 inclu

Structure-based Drug Discovery
Author : Harren Jhoti,Andrew R. Leach
Publisher : Springer Science & Business Media
Release Date : 2007-05-24
ISBN 10 : 1402044070
Pages : 250 pages

This book describes some of the most exciting developments for the discovery of new drugs, such as Fragment-based methods. It contains the latest developments in technologies that can be used to obtain the 3-D structures. This book includes experimental approaches using X-ray crystallography and NMR for Fragment-based screening as well as other biophysical methods for studying protein/ligand interactions.

Science of Synthesis: Biocatalysis in Organic Synthesis Vol. 2
Author : N.A
Publisher : Georg Thieme Verlag
Release Date : 2015-03-11
ISBN 10 : 313176631X
Pages : 672 pages

The three Science of Synthesis volumes on "Biocatalysis in Organic Synthesis" are designed to present the new possibilities offered by modern biocatalysis to the nonspecialist academic and industrial readership who are involved in practical organic synthesis. The goal of the reference work is to help start a new wave of enthusiasm for biocatalysis in the broader community and to give an overview of the field. As is the case with all of the Science of Synthesis volumes, "Biocatalysis in Organic Synthesis" offers critical reviews of organic transformations by experts, including typical or general experimental procedures. The content organization of the three volumes is based on the type of reaction performed under biocatalysis. Volume 2 covers reactions involving the formation of C-C bonds. Addition of carbon nucleophiles at C-O and C-N double bonds are reviewed, as are methods for the formation of C-C bonds at arenes and additions to C-C double bonds. Other chapters present transamination and reductive amination reactions, reduction of carbonyl compounds, and the chemistry of epoxides

Science of Synthesis: Biocatalysis in Organic Synthesis Vol. 1
Author : N.A
Publisher : Georg Thieme Verlag
Release Date : 2015-03-11
ISBN 10 : 3131766115
Pages : 648 pages

The three Science of Synthesis volumes on "Biocatalysis in Organic Synthesis" are designed to present the new possibilities offered by modern biocatalysis to the nonspecialist academic and industrial readership who are involved in practical organic synthesis. The goal of the reference work is to help start a new wave of enthusiasm for biocatalysis in the broader community and to give an overview of the field. As is the case with all of the Science of Synthesis volumes, "Biocatalysis in Organic Synthesis" offers critical reviews of organic transformations by experts, including typical or general experimental procedures. The content organization of the three volumes is based on the type of reaction performed under biocatalysis. Volume 1 begins with chapters discussing the historical development of the field, sources of enzymes and appropriate selection of catalysts, and general strategies employed in biocatalysis. This is followed by reviews of the biocatalytic hydrolysis of various substrates. The volume concludes with chapters devoted to biocatalytic isomerizations, and the synthesis of glycosides.

Chemoinformatics Approaches to Virtual Screening
Author : Alexandre Varnek,Alex Tropsha
Publisher : Royal Society of Chemistry
Release Date : 2008
ISBN 10 : 0854041443
Pages : 338 pages

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.

The Handbook of Metabolic Phenotyping
Author : John C. Lindon,Jeremy K. Nicholson,Elaine Holmes
Publisher : Elsevier
Release Date : 2018-10-04
ISBN 10 : 0128122943
Pages : 619 pages

The Handbook of Metabolic Phenotyping is the definitive work on the rapidly developing subject of metabolic phenotyping. It explores in detail the wide array of analytical chemistry and statistical modeling techniques used in the field, coupled with surveys of the various application areas in human development, nutrition, disease, therapy, and epidemiology to create a comprehensive exploration of the area of study. It covers recent studies that integrate the various -omics data sets to derive a systems biology view. It also addresses current issues on standardization, assay and statistics validation, and data storage and sharing. Written by experts with many years of practice in the field who pioneered many of the approaches widely used today, The Handbook of Metabolic Phenotyping is a valuable resource for postgrads and research scientists studying and furthering the field of metabolomics. Contains theoretical and practical explanations of all the main analytical chemistry techniques used in metabolic phenotyping Explores, in detail, the many diverse statistical approaches used in the field Offers practical tips for successfully conducting metabolic phenotyping studies Features reviews of all of the various fields of activity relating to human studies

Fragment-based Approaches in Drug Discovery
Author : Wolfgang Jahnke,Daniel A. Erlanson
Publisher : John Wiley & Sons
Release Date : 2006-12-13
ISBN 10 : 3527608605
Pages : 391 pages

This first systematic summary of the impact of fragment-based approaches on the drug development process provides essential information that was previously unavailable. Adopting a practice-oriented approach, this represents a book by professionals for professionals, tailor-made for drug developers in the pharma and biotech sector who need to keep up-to-date on the latest technologies and strategies in pharmaceutical ligand design. The book is clearly divided into three sections on ligand design, spectroscopic techniques, and screening and drug discovery, backed by numerous case studies.

Ring Theory and Its Applications
Author : Dinh Van Huynh, S. K. Jain, Sergio R. López-Permouth,S. Tariq Rizvi,Cosmin S. Roman
Publisher : American Mathematical Soc.
Release Date : 2014-02-21
ISBN 10 : 0821887971
Pages : 311 pages

This volume contains the proceedings of the Ring Theory Session in honor of T. Y. Lam's 70th birthday, at the 31st Ohio State-Denison Mathematics Conference, held from May 25-27, 2012, at The Ohio State University, Columbus, Ohio. Included are expository articles and research papers covering topics such as cyclically presented modules, Eggert's conjecture, the Mittag-Leffler conditions, clean rings, McCoy rings, QF rings, projective and injective modules, Baer modules, and Leavitt path algebras. Graduate students and researchers in many areas of algebra will find this volume valuable as the papers point out many directions for future work; in particular, several articles contain explicit lists of open questions.

De novo Molecular Design
Author : Gisbert Schneider
Publisher : Wiley-VCH
Release Date : 2013-12-23
ISBN 10 : 9783527334612
Pages : 576 pages

Systematically examining current methods and strategies, this ready reference covers a wide range of molecular structures, from organic-chemical drugs to peptides, Proteins and nucleic acids, in line with emerging new drug classes derived from biomacromolecules. A leader in the field and one of the pioneers of this young discipline has assembled here the most prominent experts from across the world to provide first-hand knowledge. While most of their methods and examples come from the area of pharmaceutical discovery and development, the approaches are equally applicable for chemical probes and diagnostics, pesticides, and any other molecule designed to interact with a biological system. Numerous images and screenshots illustrate the many examples and method descriptions. With its broad and balanced coverage, this will be the firststop resource not only for medicinal chemists, biochemists and biotechnologists, but equally for bioinformaticians and molecular designers for many years to come. From the content: * Reaction-driven de novo design * Adaptive methods in molecular design * Design of ligands against multitarget profiles * Free energy methods in ligand design * Fragment-based de novo design * Automated design of focused and target family-oriented compound libraries * Molecular de novo design by nature-inspired computing * 3D QSAR approaches to de novo drug design * Bioisosteres in de novo design * De novo design of peptides, proteins and nucleic acid structures, including RNA aptamers and many more.

Computational Approaches in Cheminformatics and Bioinformatics
Author : Rajarshi Guha,Andreas Bender
Publisher : John Wiley & Sons
Release Date : 2011-11-30
ISBN 10 : 1118131428
Pages : 288 pages

A breakthrough guide employing knowledge that unites cheminformatics and bioinformatics as innovation for the future Bridging the gap between cheminformatics and bioinformatics for the first time, Computational Approaches in Cheminformatics and Bioinformatics provides insight on how to blend these two sciences for progressive research benefits. It describes the development and evolution of these fields, how chemical information may be used for biological relations and vice versa, the implications of these new connections, and foreseeable developments in the future. Using algorithms and domains as workflow tools, this revolutionary text drives bioinformaticians to consider chemical structure, and similarly, encourages cheminformaticians to consider large biological systems such as protein targets and networks. Computational Approaches in Cheminformatics and Bioinformatics covers: Data sources available for modelling and prediction purposes Developments of conventional Quantitative Structure-Activity Relationships (QSAR) Computational tools for manipulating chemical and biological data Novel ways of probing the interactions between small molecules and proteins Also including insight from public (NIH), academic, and industrial sources (Novartis, Pfizer), this book offers expert knowledge to aid scientists through industry and academic study. The invaluable applications for drug discovery, cellular and molecular biology, enzymology, and metabolism make Computational Approaches in Cheminformatics and Bioinformatics the essential guidebook for evolving drug discovery research and alleviating the issue of chemical control and manipulation of various systems.

Methods and Algorithms for Molecular Docking-Based Drug Design and Discovery
Author : Dastmalchi, Siavoush
Publisher : IGI Global
Release Date : 2016-05-03
ISBN 10 : 1522501169
Pages : 456 pages

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 Discovery
Author : Steven Howard,Chris Abell
Publisher : Royal Society of Chemistry
Release Date : 2015-07-03
ISBN 10 : 1849739080
Pages : 264 pages

Fragment-based drug discovery is a rapidly evolving area of research, which has recently seen new applications in areas such as epigenetics, GPCRs and the identification of novel allosteric binding pockets. The first fragment-derived drug was recently approved for the treatment of melanoma. It is hoped that this approval is just the beginning of the many drugs yet to be discovered using this fascinating technique. This book is written from a Chemist's perspective and comprehensively assesses the impact of fragment-based drug discovery on a wide variety of areas of medicinal chemistry. It will prove to be an invaluable resource for medicinal chemists working in academia and industry, as well as anyone interested in novel drug discovery techniques.