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From Chemical Topology To Three Dimensional Geometry
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Book Synopsis From Chemical Topology to Three-Dimensional Geometry by : Alexandru T. Balaban
Download or read book From Chemical Topology to Three-Dimensional Geometry written by Alexandru T. Balaban and published by Springer Science & Business Media. This book was released on 2006-04-11 with total page 420 pages. Available in PDF, EPUB and Kindle. Book excerpt: Even high-speed supercomputers cannot easily convert traditional two-dimensional databases from chemical topology into the three-dimensional ones demanded by today's chemists, particularly those working in drug design. This fascinating volume resolves this problem by positing mathematical and topological models which greatly expand the capabilities of chemical graph theory. The authors examine QSAR and molecular similarity studies, the relationship between the sequence of amino acids and the less familiar secondary and tertiary protein structures, and new topological methods.
Download or read book Chemical Topology written by D Bonchev and published by CRC Press. This book was released on 1999-04-23 with total page 354 pages. Available in PDF, EPUB and Kindle. Book excerpt: Topology is becoming increasingly important in chemistry because of its rapidly growing number of applications. Here, its many uses are reviewed and the authors anticipate what future developments might bring. This work shows how significant new insights can be gained by representing molecular species as topological structures known as topographs. The text explores carbon structures, establishing how the stability of fullerene species can be accounted for and also predicting which fullerenes will be most stable. It is pointed out that molecular topology, rather than molecular geometry, characterizes molecular shape and various tools for shape characterization are described. Several of the fascinating ideas that arise from regarding topology as a unifying principle in chemical bonding theory are discussed, and in particular, the novel concept of the molecular topoid is shown to have numerous uses. The topological description of polymers is examined and the reader is gently guided through the realms of branched and tangled polymers. Overall, this work outlines the fact that topology is not only a theoretical discipline but also one that has practical applications and high relevance to the whole domain of chemistry.
Book Synopsis Three Dimensional QSAR by : Jean Pierre Doucet
Download or read book Three Dimensional QSAR written by Jean Pierre Doucet and published by CRC Press. This book was released on 2010-12-17 with total page 575 pages. Available in PDF, EPUB and Kindle. Book excerpt: As a result of new statistical and mathematical approaches, improved visualization tools, and recognition by international regulatory groups, quantitative structure-activity relationships (QSARs) now play important roles in pharmacology for the design of new drugs as well as in toxicology and ecotoxicology for hazard identification and risk assessment. Providing up-to-date coverage of the field, Three Dimensional QSAR: Applications in Pharmacology and Toxicology presents the most recent QSAR methods and illustrates their scope, advantages, and limitations. Part I The first part of the book addresses CoMFA and related methods, such as CoMSIA, FLUFF, SOMFA. It also describes shape-, surface-, and volume-based approaches, including MSA, excluded volume, LIV, HASL, receptor surface model, COMPASS, and CoMSA. Part II Focusing on methods that use 3D information, the second part covers autocorrelation methods, such as GRIND; similarity-based methods, including similarity matrices and quantum similarity indices; and quantitative spectroscopic data–activity relationships. Some applications in data mining are also explored. Part III The third part deals with post-3D models. The authors discuss the adaptation of the receptor and simultaneous presence of several conformers or solvation mechanisms. Part IV The final part presents receptor-related approaches as well as docking and free energy calculations, which are treated at various levels. This part concerns the extensive sampling of phase space and approximate methods, such as linear interaction energy, Poisson–Boltzmann, and generalized Born models. A case study covering several parallel approaches is also developed. An appendix offers the basic principles of modeling and statistical tools routinely required in QSAR methodologies, including optimization methods, molecular mechanics and dynamics, multivariate analysis, nonlinear models, and evolutionary techniques. It provides newcomers with the concepts necessary to fully grasp the essentials of these methods and gives a basic grounding in their correct use. Illustrated with numerous examples and a color insert, this book supplies a clear overview of the strengths and weaknesses of 3D-QSAR approaches. It explains how these modern techniques can link the biological activity of chemicals to their structure, encompassing both their 2D structural formulae and 3D geometry.
Book Synopsis Topological Indices and Related Descriptors in QSAR and QSPR by : James Devillers
Download or read book Topological Indices and Related Descriptors in QSAR and QSPR written by James Devillers and published by CRC Press. This book was released on 2000-03-09 with total page 811 pages. Available in PDF, EPUB and Kindle. Book excerpt: Topological Indices and Related Descriptors in QSAR and QSPR reviews the state of the art in this field and highlights the important advances in the generation of descriptors calculated directly from the structure of molecules. This long-awaited comprehensive book provides all the necessary information to calculate and use these descriptors for deriving structure-activity and structure-property relationships. Written by leading experts in the field, this book discusses the physicochemical significance, strengths, and weaknesses of these indices and presents numerous examples of applications. This book will be a valuable reference for anyone involved in the use of QSAR and QSPR in the pharmaceutical, applied chemical, and environmental sciences. It is also suitable for use as a supplementary textbook on related graduate level courses.
Book Synopsis Advances in Dendritic Macromolecules by : G.R. Newkome
Download or read book Advances in Dendritic Macromolecules written by G.R. Newkome and published by Elsevier. This book was released on 1999-08-31 with total page 206 pages. Available in PDF, EPUB and Kindle. Book excerpt: The series Advances in Dendritic Macromolecules aims to cover the synthesis and supramolecular chemistry of dendritic or cascade super-molecules as well as their less perfect hyperbranched cousins. The field of hyperbranched macromolecules, specifically dendrimers, has continued to expand at an amazing rate. The synthetic aspects, which were assumed to be over several years ago, have opened new avenues into the mesomolecular regime. The synthetic ingenuity of chemical artists has afforded new monomers and their diverse combinations to give rise to (poly)functionalized materials that embrace new supramolecular concepts in areas such as molecular recognition, assembly, encapsulation, and inclusion; catalysts; coatings; drug delivery systems; and in essence opens up the field of suprasupermolecular chemistry. In chapter 1 the synthesis of organometallic and related transition metal-cotaining dendrimers is summarized and their novel properties and useful applications are described. Chapter 2 covers work on the commercial poly(propylene imine)s, including the "dendritic box", dendrimer-based superamphiphiles, and unimolecular inverse micelles. The next chapter looks at aspects of chirality in dendritic systems and this is followed by a look inside dendrimers from a molecular topologist's point-of-view.
Book Synopsis Solved and Unsolved Problems of Structural Chemistry by : Milan Randic
Download or read book Solved and Unsolved Problems of Structural Chemistry written by Milan Randic and published by CRC Press. This book was released on 2016-04-21 with total page 472 pages. Available in PDF, EPUB and Kindle. Book excerpt: Solved and Unsolved Problems of Structural Chemistry introduces new methods and approaches for solving problems related to molecular structure. It includes numerous subjects such as aromaticity—one of the central themes of chemistry—and topics from bioinformatics such as graphical and numerical characterization of DNA, proteins, and proteomes. It also outlines the construction of novel tools using techniques from discrete mathematics, particularly graph theory, which allowed problems to be solved that many had considered unsolvable. The book discusses a number of important problems in chemistry that have not been fully understood or fully appreciated, such as the notion of aromaticity and conjugated circuits, the generalized Hückel 4n + 2 Rule, and the nature of quantitative structure–property–activity relationships (QSARs), which have resulted in only partially solved problems and approximated solutions that are inadequate. It also describes advantages of mathematical descriptors in QSAR, including their use in screening combinatorial libraries to search for structures with high similarity to the target compounds. Selected problems that this book addresses include: Multiple regression analysis (MRA) Insufficient use of partial ordering in chemistry The role of Kekulé valence structures The problem of protein and DNA alignment Solved and Unsolved Problems of Structural Chemistry collects results that were once scattered in scientific literature into a thoughtful and compact volume. It sheds light on numerous problems in chemistry, including ones that appeared to have been solved but were actually only partially solved. Most importantly, it shows more complete solutions as well as methods and approaches that can lead to actualization of further solutions to problems in chemistry.
Book Synopsis Handbook of Molecular Descriptors by : Roberto Todeschini
Download or read book Handbook of Molecular Descriptors written by Roberto Todeschini and published by John Wiley & Sons. This book was released on 2008-07-11 with total page 688 pages. Available in PDF, EPUB and Kindle. Book excerpt: Quantitative studies on structure-activity and structure-property relationships are powerful tools in directed drug research. In recent years, various strategies have been developed to characterize and classify structural patterns by means of molecular descriptors. It has become possible not only to assess diversities or similarities of structure databases, but molecular descriptors also facilitate the identification of potential bioactive molecules from the rapidly increasing number of compound libraries. They even allow for a controlled de-novo design of new lead structures. This is the most comprehensive collection of molecular descriptors and presents a detailed review from the origins of this research field up to present day. This practically oriented reference book gives a thorough overview of the different molecular descriptors representations and their corresponding molecular descriptors. All descriptors are listed with their definition, symbols and labels, formulas, some numerical examples, data and molecular graphs, while numerous figures and tables aid comprehension of the definitions. Cross-references throughout, a list of acronyms and notations allow easy access to the information needed to solve a specific research problem. Examples of descriptor calculations along with tables of descriptor values for a set of selected reference compounds and an up-to-date reference list add to the practical value of the book, making it an invaluable guide for all those dealing with bioactive molecules as well as for researchers.
Book Synopsis Molecular Descriptors for Chemoinformatics by : Roberto Todeschini
Download or read book Molecular Descriptors for Chemoinformatics written by Roberto Todeschini and published by John Wiley & Sons. This book was released on 2009-10-30 with total page 1257 pages. Available in PDF, EPUB and Kindle. Book excerpt: The number-one reference on the topic now contains a wealth of new data: The entire relevant literature over the past six years has been painstakingly surveyed, resulting in hundreds of new descriptors being added to the list, and some 3,000 new references in the bibliography section. Volume 1 contains an alphabetical listing of more than 3300 descriptors and related terms for chemoinformatic analysis of chemical compound properties, while the second volume lists over 6,000 references selected from 450 journals. To make the data even more accessible, the introductory section has been completely re-written and now contains several "walk-through" reading lists of selected keywords for novice users.
Book Synopsis Three-Dimensional Geometry and Topology, Volume 1 by : William P. Thurston
Download or read book Three-Dimensional Geometry and Topology, Volume 1 written by William P. Thurston and published by Princeton University Press. This book was released on 2014-10-31 with total page 323 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book develops some of the extraordinary richness, beauty, and power of geometry in two and three dimensions, and the strong connection of geometry with topology. Hyperbolic geometry is the star. A strong effort has been made to convey not just denatured formal reasoning (definitions, theorems, and proofs), but a living feeling for the subject. There are many figures, examples, and exercises of varying difficulty. This book was the origin of a grand scheme developed by Thurston that is now coming to fruition. In the 1920s and 1930s the mathematics of two-dimensional spaces was formalized. It was Thurston's goal to do the same for three-dimensional spaces. To do this, he had to establish the strong connection of geometry to topology--the study of qualitative questions about geometrical structures. The author created a new set of concepts, and the expression "Thurston-type geometry" has become a commonplace. Three-Dimensional Geometry and Topology had its origins in the form of notes for a graduate course the author taught at Princeton University between 1978 and 1980. Thurston shared his notes, duplicating and sending them to whoever requested them. Eventually, the mailing list grew to more than one thousand names. The book is the culmination of two decades of research and has become the most important and influential text in the field. Its content also provided the methods needed to solve one of mathematics' oldest unsolved problems--the Poincaré Conjecture. In 2005 Thurston won the first AMS Book Prize, for Three-dimensional Geometry and Topology. The prize recognizes an outstanding research book that makes a seminal contribution to the research literature. Thurston received the Fields Medal, the mathematical equivalent of the Nobel Prize, in 1982 for the depth and originality of his contributions to mathematics. In 1979 he was awarded the Alan T. Waterman Award, which recognizes an outstanding young researcher in any field of science or engineering supported by the National Science Foundation.
Book Synopsis Topology in Chemistry by : D H Rouvray
Download or read book Topology in Chemistry written by D H Rouvray and published by Elsevier. This book was released on 2002-04-01 with total page 400 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume addresses a number of topological themes of direct relevance to chemists. Topological concepts are now regularly applied in wide areas of chemistry including molecular engineering and design, chemical toxicology, the study of molecular shape, crystal and surface structures, chemical bonding, macromolecular species such as polymers and DNA, and environmental chemistry. Currently, the design and synthesis of new drugs and agrochemicals are of especial importance. The book's prime focus is on the role played by topological indices in the description and characterisation of molecular species. The Wiener index along with a variety of other major topological indices, are discussed with particular reference to the powerful and much used connectivity indices. In this book an international team of leading experts review their respective fields and present their findings.The considerable benefits offered by topological indices in the investigation of chemical problems in science, medicine, and industry are highlighted. The volume records proceedings of the Harry Wiener Memorial Conference on the Role of Topology in Chemistry, held at the University of Georgia in March 2001, and serves as a fitting tribute to the chemical contributions of the late Harry Wiener. Focuses on the role played by topological indices in the description and characterisation of molecular species Records the proceedings of the Harry Weiner Memorial Conference on the Role of Topology in Chemistry, held at the University of Georgia in March 2001 Along with a variety of other major topological indices, the Wiener index is discussed with particular reference to the powerful and much-used connectivity indices
Book Synopsis Progress in Biological Chirality by : Gyula Palyi
Download or read book Progress in Biological Chirality written by Gyula Palyi and published by Elsevier. This book was released on 2004-12-13 with total page 444 pages. Available in PDF, EPUB and Kindle. Book excerpt: Following on from Advances in BioChirality, Progress in Biological Chirality provides a unique summary and review of the most recent developments in the field of biochirality. Living organisms use only one enantiomer of chiral molecules in the majority of biologically important processes. The exact origin and mechanisms for this surprising selectivity are not yet known. This book discusses current research aimed at identifying the scientific reasons that may contribute to this phenomenon. Progress in Biological Chirality takes an interdisciplinary approach to this exciting field, covering a wide range of topics, such as, theory, palaeontology and food technology, to name but a few. This book presents findings via a broad spectrum of scientific approaches making it an excellent overview of Biological Chirality, suitable for postgraduate students, practitioners and researchers in the field of chemistry, biochemistry, biology, palaeontology, and food science with an interest in Chirality. This book contains 32 chapters written by Authors, who are leading authorities in the field Presents the most recent research taking place in this highly challenging field Contains both reference material for the specialist and provides an overview for those who are interested in the fundamental problems of biology and chemistry
Book Synopsis Statistical Modelling of Molecular Descriptors in QSAR/QSPR by : Matthias Dehmer
Download or read book Statistical Modelling of Molecular Descriptors in QSAR/QSPR written by Matthias Dehmer and published by John Wiley & Sons. This book was released on 2012-09-13 with total page 437 pages. Available in PDF, EPUB and Kindle. Book excerpt: This handbook and ready reference presents a combination of statistical, information-theoretic, and data analysis methods to meet the challenge of designing empirical models involving molecular descriptors within bioinformatics. The topics range from investigating information processing in chemical and biological networks to studying statistical and information-theoretic techniques for analyzing chemical structures to employing data analysis and machine learning techniques for QSAR/QSPR. The high-profile international author and editor team ensures excellent coverage of the topic, making this a must-have for everyone working in chemoinformatics and structure-oriented drug design.
Book Synopsis Molecular Modeling and Prediction of Bioactivity by : Klaus Gundertofte
Download or read book Molecular Modeling and Prediction of Bioactivity written by Klaus Gundertofte and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 490 pages. Available in PDF, EPUB and Kindle. Book excerpt: Much of chemistry, molecular biology, and drug design, are centered around the relationships between chemical structure and measured properties of compounds and polymers, such as viscosity, acidity, solubility, toxicity, enzyme binding, and membrane penetration. For any set of compounds, these relationships are by necessity complicated, particularly when the properties are of biological nature. To investigate and utilize such complicated relationships, henceforth abbreviated SAR for structure-activity relationships, and QSAR for quantitative SAR, we need a description of the variation in chemical structure of relevant compounds and biological targets, good measures of the biological properties, and, of course, an ability to synthesize compounds of interest. In addition, we need reasonable ways to construct and express the relationships, i. e. , mathematical or other models, as well as ways to select the compounds to be investigated so that the resulting QSAR indeed is informative and useful for the stated purposes. In the present context, these purposes typically are the conceptual understanding of the SAR, and the ability to propose new compounds with improved property profiles. Here we discuss the two latter parts of the SARlQSAR problem, i. e. , reasonable ways to model the relationships, and how to select compounds to make the models as "good" as possible. The second is often called the problem of statistical experimental design, which in the present context we call statistical molecular design, SMD. 1.
Book Synopsis Advances in Mathematical Chemistry and Applications: Volume 1 by : Subhash C. Basak
Download or read book Advances in Mathematical Chemistry and Applications: Volume 1 written by Subhash C. Basak and published by Elsevier. This book was released on 2016-02-11 with total page 378 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in Mathematical Chemistry and Applications highlights the recent progress in the emerging discipline of discrete mathematical chemistry. Editors Subhash C. Basak, Guillermo Restrepo, and Jose Luis Villaveces have brought together 27 chapters written by 68 internationally renowned experts in these two volumes. Each volume comprises a wise integration of mathematical and chemical concepts and covers numerous applications in the field of drug discovery, bioinformatics, chemoinformatics, computational biology, mathematical proteomics, and ecotoxicology. Volume 1 includes chapters on mathematical structural descriptors of molecules and biomolecules, applications of partially ordered sets (posets) in chemistry, optimal characterization of molecular complexity using graph theory, different connectivity matrices and their polynomials, use of 2D fingerprints in similarity-based virtual screening, mathematical approaches to molecular structure generation, comparability graphs, applications of molecular topology in drug design, density functional theory of chemical reactivity, application of mathematical descriptors in the quantification of drug-likeness, utility of pharmacophores in drug design, and much more. Brings together both the theoretical and practical aspects of the fundamental concepts of mathematical chemistry Covers applications in diverse areas of physics, chemistry, drug discovery, predictive toxicology, systems biology, chemoinformatics, and bioinformatics Revised 2015 edition includes a new chapter on the current landscape of hierarchical QSAR modelling About half of the book focuses primarily on current work, new applications, and emerging approaches for the mathematical characterization of essential aspects of molecular structure, while the other half describes applications of structural approach to new drug discovery, virtual screening, protein folding, predictive toxicology, DNA structure, and systems biology
Book Synopsis Recent Advances in QSAR Studies by : Tomasz Puzyn
Download or read book Recent Advances in QSAR Studies written by Tomasz Puzyn and published by Springer Science & Business Media. This book was released on 2010-01-19 with total page 428 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents an interdisciplinary overview on the most recent advances in QSAR studies. The first part consists of a comprehensive review of QSAR methodology. The second part highlights the interdisciplinary aspects and new areas of QSAR modelling.
Book Synopsis Periodic Nanostructures by : Mircea V. Diudea
Download or read book Periodic Nanostructures written by Mircea V. Diudea and published by Springer Science & Business Media. This book was released on 2007-08-23 with total page 209 pages. Available in PDF, EPUB and Kindle. Book excerpt: These tiny structures could offer architectural designs for the cities of the future. The authors explore the foam-like carbon structures, which relate to ‘schwarzites’ and which are infinite periodic minimal surfaces of negative curvature. They show that the periodicity of close repeat units of such structures is evident not only in these formations but also in all of the carbon allotropes. The text provides literature and data on the field of nanostructure periodicity and the authors’ own results on nanostructure building and energy calculations.
Book Synopsis Cheminformatics, QSAR and Machine Learning Applications for Novel Drug Development by : Kunal Roy
Download or read book Cheminformatics, QSAR and Machine Learning Applications for Novel Drug Development written by Kunal Roy and published by Elsevier. This book was released on 2023-05-23 with total page 768 pages. Available in PDF, EPUB and Kindle. Book excerpt: Cheminformatics, QSAR and Machine Learning Applications for Novel Drug Development aims at showcasing different structure-based, ligand-based, and machine learning tools currently used in drug design. It also highlights special topics of computational drug design together with the available tools and databases. The integrated presentation of chemometrics, cheminformatics, and machine learning methods under is one of the strengths of the book.The first part of the content is devoted to establishing the foundations of the area. Here recent trends in computational modeling of drugs are presented. Other topics present in this part include QSAR in medicinal chemistry, structure-based methods, chemoinformatics and chemometric approaches, and machine learning methods in drug design. The second part focuses on methods and case studies including molecular descriptors, molecular similarity, structure-based based screening, homology modeling in protein structure predictions, molecular docking, stability of drug receptor interactions, deep learning and support vector machine in drug design. The third part of the book is dedicated to special topics, including dedicated chapters on topics ranging from de design of green pharmaceuticals to computational toxicology. The final part is dedicated to present the available tools and databases, including QSAR databases, free tools and databases in ligand and structure-based drug design, and machine learning resources for drug design. The final chapters discuss different web servers used for identification of various drug candidates. Presents chemometrics, cheminformatics and machine learning methods under a single reference Showcases the different structure-based, ligand-based and machine learning tools currently used in drug design Highlights special topics of computational drug design and available tools and databases
