A Primer on QSAR/QSPR Modeling

A Primer on QSAR/QSPR Modeling
Author: Kunal Roy
Publisher: Springer
Total Pages: 129
Release: 2015-04-11
Genre: Science
ISBN: 3319172816

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This brief goes back to basics and describes the Quantitative structure-activity/property relationships (QSARs/QSPRs) that represent predictive models derived from the application of statistical tools correlating biological activity (including therapeutic and toxic) and properties of chemicals (drugs/toxicants/environmental pollutants) with descriptors representative of molecular structure and/or properties. It explains how the sub-discipline of Cheminformatics is used for many applications such as risk assessment, toxicity prediction, property prediction and regulatory decisions apart from drug discovery and lead optimization. The authors also present, in basic terms, how QSARs and related chemometric tools are extensively involved in medicinal chemistry, environmental chemistry and agricultural chemistry for ranking of potential compounds and prioritizing experiments. At present, there is no standard or introductory publication available that introduces this important topic to students of chemistry and pharmacy. With this in mind, the authors have carefully compiled this brief in order to provide a thorough and painless introduction to the fundamental concepts of QSAR/QSPR modelling. The brief is aimed at novice readers.

Statistical Modelling of Molecular Descriptors in QSAR/QSPR

Statistical Modelling of Molecular Descriptors in QSAR/QSPR
Author: Matthias Dehmer
Publisher: John Wiley & Sons
Total Pages: 437
Release: 2012-09-13
Genre: Medical
ISBN: 3527645012

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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.

QSPR/QSAR Analysis Using SMILES and Quasi-SMILES

QSPR/QSAR Analysis Using SMILES and Quasi-SMILES
Author: Alla P. Toropova
Publisher: Springer Nature
Total Pages: 470
Release: 2023-06-10
Genre: Science
ISBN: 3031284011

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This contributed volume overviews recently presented approaches for carrying out QSPR/QSAR analysis by using a simplifying molecular input-line entry system (SMILES) to represent the molecular structure. In contrast to traditional SMILES, quasi-SMILES is a sequence of special symbols-codes that reflect molecular features and codes of experimental conditions. SMILES and quasi-SMILES serve as a basis to develop QSPR/QSAR as well Nano-QSPR/QSAR via the Monte Carlo calculation that provides the so-called optimal descriptors for QSPR/QSAR models. The book presents a reliable technology for developing Nano-QSPR/QSAR while it also includes the description of the algorithms of the Monte Carlo optimization. It discusses the theory and practice of the technique of variational authodecoders (VAEs) based on SMILES and analyses in detail the index of ideality of correlation (IIC) and the correlation intensity index (CII) which are new criteria for the predictive potential of the model. The mathematical apparatus used is simple so that students of relevant specializations can easily follow. This volume is a valuable contribution to the field and will be of great interest to developers of models of physicochemical properties and biological activity, chemical technologists, and toxicologists involved in the area of drug design.

Fragmentation: Toward Accurate Calculations on Complex Molecular Systems

Fragmentation: Toward Accurate Calculations on Complex Molecular Systems
Author: Mark S. Gordon
Publisher: John Wiley & Sons
Total Pages: 376
Release: 2017-10-23
Genre: Science
ISBN: 1119129249

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Fragmentation: Toward Accurate Calculations on Complex Molecular Systems introduces the reader to the broad array of fragmentation and embedding methods that are currently available or under development to facilitate accurate calculations on large, complex systems such as proteins, polymers, liquids and nanoparticles. These methods work by subdividing a system into subunits, called fragments or subsystems or domains. Calculations are performed on each fragment and then the results are combined to predict properties for the whole system. Topics covered include: Fragmentation methods Embedding methods Explicitly correlated local electron correlation methods Fragment molecular orbital method Methods for treating large molecules This book is aimed at academic researchers who are interested in computational chemistry, computational biology, computational materials science and related fields, as well as graduate students in these fields.

Understanding the Basics of QSAR for Applications in Pharmaceutical Sciences and Risk Assessment

Understanding the Basics of QSAR for Applications in Pharmaceutical Sciences and Risk Assessment
Author: Kunal Roy
Publisher: Academic Press
Total Pages: 494
Release: 2015-03-03
Genre: Medical
ISBN: 0128016337

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Understanding the Basics of QSAR for Applications in Pharmaceutical Sciences and Risk Assessment describes the historical evolution of quantitative structure-activity relationship (QSAR) approaches and their fundamental principles. This book includes clear, introductory coverage of the statistical methods applied in QSAR and new QSAR techniques, such as HQSAR and G-QSAR. Containing real-world examples that illustrate important methodologies, this book identifies QSAR as a valuable tool for many different applications, including drug discovery, predictive toxicology and risk assessment. Written in a straightforward and engaging manner, this is the ideal resource for all those looking for general and practical knowledge of QSAR methods. Includes numerous practical examples related to QSAR methods and applications Follows the Organization for Economic Co-operation and Development principles for QSAR model development Discusses related techniques such as structure-based design and the combination of structure- and ligand-based design tools

Quantum Modeling of Complex Molecular Systems

Quantum Modeling of Complex Molecular Systems
Author: Jean-Louis Rivail
Publisher: Springer
Total Pages: 524
Release: 2015-10-13
Genre: Science
ISBN: 3319216260

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This multi-author contributed volume includes methodological advances and original applications to actual chemical or biochemical phenomena which were not possible before the increased sophistication of modern computers. The chapters contain detailed reviews of the developments of various computational techniques, used to study complex molecular systems such as molecular liquids and solutions (particularly aqueous solutions), liquid-gas, solid-gas interphase and biomacromolecular systems. Quantum modeling of complex molecular systems is a useful resource for graduate students and fledgling researchers and is also an excellent companion for research professionals engaged in computational chemistry, material science, nanotechnology, physics, drug design, and molecular biochemistry.

Computational Approaches in Cheminformatics and Bioinformatics

Computational Approaches in Cheminformatics and Bioinformatics
Author: Rajarshi Guha
Publisher: John Wiley & Sons
Total Pages: 299
Release: 2012-01-04
Genre: Science
ISBN: 0470384417

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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.

Chemoinformatics and Advanced Machine Learning Perspectives: Complex Computational Methods and Collaborative Techniques

Chemoinformatics and Advanced Machine Learning Perspectives: Complex Computational Methods and Collaborative Techniques
Author: Lodhi, Huma
Publisher: IGI Global
Total Pages: 418
Release: 2010-07-31
Genre: Computers
ISBN: 1615209123

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"This book is a timely compendium of key elements that are crucial for the study of machine learning in chemoinformatics, giving an overview of current research in machine learning and their applications to chemoinformatics tasks"--Provided by publisher.

Prediction of Properties of Low and High Molecular Weight Compounds

Prediction of Properties of Low and High Molecular Weight Compounds
Author: Carlo Giuseppe Bertinetto
Publisher: LAP Lambert Academic Publishing
Total Pages: 192
Release: 2012
Genre:
ISBN: 9783659271090

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This work describes and discusses an innovative approach for the prediction of physical, chemical and biological properties of compounds, ranging from small molecules to large polymers. It is based on the direct and adaptive treatment of molecular structure by means of a Recursive Neural Network (RNN) to derive Quantitative Structure-Property/Activity Relationships (QSPR/QSARs). Chemical compounds are represented through appropriate graphical tools that bypass the need for numerical descriptors. The capabilities of this methodology are investigated by applying it to different predictive problems: the melting point of ionic liquids, the glass transition temperature of polymers and the toxicity of organic molecules. The results show that the graphical molecular representation was able to effectively model each case, providing accurate predictions using practically no background knowledge. The proposed structure-based RNN approach, it is argued, can provide a simple and general prediction method with great potential in molecular design, toxicology and evaluation of other complex properties.