Cheminformatics QSAR and Machine Learning Applications for Novel Drug Development

Cheminformatics  QSAR and Machine Learning Applications for Novel Drug Development
Author: Kunal Roy
Publsiher: Elsevier
Total Pages: 768
Release: 2023-05-23
Genre: Business & Economics
ISBN: 9780443186394

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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

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,Supratik Kar,Rudra Narayan Das
Publsiher: Academic Press
Total Pages: 484
Release: 2015-03-03
Genre: Medical
ISBN: 9780128016336

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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

Computational Drug Discovery and Design

Computational Drug Discovery and Design
Author: Mohini Gore,Umesh B. Jagtap
Publsiher: Springer Nature
Total Pages: 357
Release: 2023-10-09
Genre: Medical
ISBN: 9781071634417

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This second edition provides new and updated methods and techniques for identification of drug target, binding sites prediction, high- throughput virtual screening, lead discovery and optimization, conformational sampling, prediction of pharmacokinetic properties using computer-based methodologies. Chapters also focus on the application of the latest artificial intelligence technologies for computer aided drug discovery. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary methods, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Computational Drug Discovery and Design, Second Edition aims to effectively utilize computational methodologies in discovery and design of novel drugs.

CADD and Informatics in Drug Discovery

CADD and Informatics in Drug Discovery
Author: Mithun Rudrapal,Johra Khan
Publsiher: Springer Nature
Total Pages: 370
Release: 2023-05-12
Genre: Science
ISBN: 9789819913169

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This book updates knowledge on recent advances in computational, biophysical and bioinformatics tools/techniques and their practical applications in modern drug design and discovery paradigm. It also encompasses fundamental principles, advanced methodologies and applications of various CADD approaches including several cutting-edge areas; presenting recent developments covering ongoing trends in the field of computer-aided drug discovery. Having contributions by a global team of experts, the book is expected to be an ideal resource for drug discovery scientists, medicinal chemists, pharmacologists, toxicologists, phytochemists, biochemists, biologists, R&D personnel, researchers, students, teachers and those working in the field of drug discovery. It will fill the knowledge gaps that exist in the current CADD approaches and methodologies/ protocols being widely used in both academic and research practices. Further, a special focus on current status of various computational drug design approaches (SBDD, LBDD, de novo drug design, pharmacophore-based search), bioinformatics tools and databases, computational screening and modeling of phytochemicals/natural products, artificial intelligence and machine learning, and network pharmacology and systems biology would certainly guide researchers, students or readers to conduct their research in the emerging area(s) of interest. It is also expected to be highly beneficial to various stakeholders working in the pharmaceutical and biotechnology industries (R&D), the academic as well as research sectors.

Materials Science and Engineering

Materials Science and Engineering
Author: Ke Wu,Bharath Natarajan,Lisa Morkowchuk,Mike Krein,Curt M. Breneman
Publsiher: Elsevier Inc. Chapters
Total Pages: 542
Release: 2013-07-10
Genre: Technology & Engineering
ISBN: 9780128059463

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The Materials Genome Initiative (MGI) was conceived as a unified effort to capture, curate, and exploit materials structure/property information on a grand scale to enable rapid, cost-effective development of novel materials with predictable properties. While the use of “genomic” methods to facilitate property prediction, virtual design, and discovery of materials is relatively new, the concepts driving the development of materials informatics are based, solidly, on the lessons learned during the development history of cheminformatics and bioinformatics. This chapter describes some of the ways in which cheminformatics and machine learning methods have been adapted for, and utilized in, materials science and engineering applications. Examples of how materials quantitative structure–property relationship (MQSPR) models are created, validated, and utilized are presented.

Chemoinformatics Approaches to Virtual Screening

Chemoinformatics Approaches to Virtual Screening
Author: Alexandre Varnek,Alex Tropsha
Publsiher: Royal Society of Chemistry
Total Pages: 356
Release: 2008
Genre: Science
ISBN: 9780854041442

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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.

Advances in Bioinformatics

Advances in Bioinformatics
Author: Vijai Singh,Ajay Kumar
Publsiher: Springer Nature
Total Pages: 446
Release: 2021-07-31
Genre: Science
ISBN: 9789813361911

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This book presents the latest developments in bioinformatics, highlighting the importance of bioinformatics in genomics, transcriptomics, metabolism and cheminformatics analysis, as well as in drug discovery and development. It covers tools, data mining and analysis, protein analysis, computational vaccine, and drug design. Covering cheminformatics, computational evolutionary biology and the role of next-generation sequencing and neural network analysis, it also discusses the use of bioinformatics tools in the development of precision medicine. This book offers a valuable source of information for not only beginners in bioinformatics, but also for students, researchers, scientists, clinicians, practitioners, policymakers, and stakeholders who are interested in harnessing the potential of bioinformatics in many areas.

Machine Learning in Biological Sciences

Machine Learning in Biological Sciences
Author: Shyamasree Ghosh,Rathi Dasgupta
Publsiher: Springer Nature
Total Pages: 337
Release: 2022-05-04
Genre: Medical
ISBN: 9789811688812

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This book gives an overview of applications of Machine Learning (ML) in diverse fields of biological sciences, including healthcare, animal sciences, agriculture, and plant sciences. Machine learning has major applications in process modelling, computer vision, signal processing, speech recognition, and language understanding and processing and life, and health sciences. It is increasingly used in understanding DNA patterns and in precision medicine. This book is divided into eight major sections, each containing chapters that describe the application of ML in a certain field. The book begins by giving an introduction to ML and the various ML methods. It then covers interesting and timely aspects such as applications in genetics, cell biology, the study of plant-pathogen interactions, and animal behavior. The book discusses computational methods for toxicity prediction of environmental chemicals and drugs, which forms a major domain of research in the field of biology. It is of relevance to post-graduate students and researchers interested in exploring the interdisciplinary areas of use of machine learning and deep learning in life sciences.