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Title Tutorials in chemoinformatics / edited by Alexandre Varnek
Published Hoboken, NJ : John Wiley & Sons, Inc., 2017
Online access available from:
ProQuest Ebook Central    View Resource Record  

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Description 1 online resource (xix, 462 pages)
Contents Title Page ; Copyright Page; Contents; List of Contributors; Preface; About the Companion Website; Part 1 Chemical Databases; Chapter 1 Data Curation; Theoretical Background; Software; Step-by-Step Instructions ; Conclusion; References; Chapter 2 Relational Chemical Databases: Creation, Management, and Usage ; Theoretical Background; Step-by-Step Instructions ; Conclusion; References; Chapter 3 Handling of Markush Structures ; Theoretical Background; Step-by-Step Instructions ; Conclusion; References; Chapter 4 Processing of SMILES, InChI, and Hashed Fingerprints ; Theoretical Background
AlgorithmsStep-by-Step Instructions ; Conclusion; References; Part 2 Library Design; Chapter 5 Design of Diverse and Focused Compound Libraries ; Introduction; Data Acquisition; Implementation; Compound Library Creation; Compound Library Analysis; Normalization of Descriptor Values; Visualizing Descriptor Distributions; Decorrelation and Dimension Reduction; Partitioning and Diverse Subset Calculation; Partitioning; Diverse Subset Selection; Combinatorial Libraries; Combinatorial Enumeration of Compounds; Retrosynthetic Approaches to Library Design; References
Loading Structure-Data File Descriptors and Fitting Equation; Variables Selection; Consensus Model; Model Applicability Domain; n-Fold External Cross-Validation ; Saving and Loading of the Consensus Modeling Results; Statistical Parameters of the Consensus Model; Consensus Model Performance as a Function of Individual Models Acceptance Threshold; Building Consensus Model on the Entire Data Set; Loading Input Data; Loading Selected Models and Choosing their Applicability Domain; Reporting Predicted Values; Analysis of the Fragments Contributions; References
Part 3 Data Analysis and VisualizationChapter 6 Hierarchical Clustering in R ; Theoretical Background; Algorithms; Instructions; Hierarchical Clustering Using Fingerprints; Hierarchical Clustering Using Descriptors; Visualization of the Data Sets; Alternative Clustering Methods; Conclusion; References; Chapter 7 Data Visualization and Analysis Using Kohonen Self-Organizing Maps ; Theoretical Background; Algorithms; Instructions; Conclusion; References; Part 4 Obtaining and Validation QSAR/QSPR Models; Chapter 8 Descriptors Generation Using the CDK Toolkit and Web Services
Theoretical BackgroundAlgorithms; Step-by-Step Instructions ; Conclusion; References; Chapter 9 QSPR Models on Fragment Descriptors ; Abbreviations; DATA; ISIDA_QSPR input; Data Split Into Training and Test Sets; Substructure Molecular Fragment (SMF) Descriptors; Regression Equations; Forward and Backward Stepwise Variable Selection; Parameters of Internal Model Validation; Applicability Domain (AD) of the Model; Storage and Retrieval Modeling Results; Analysis of Modeling Results; Root-Mean Squared Error (RMSE) Estimation ; Setting the Parameters; Analysis of n-Fold Cross-Validation Results
Summary 30 tutorials and more than 100 exercises in chemoinformatics, supported by online software and data sets Chemoinformatics is widely used in both academic and industrial chemical and biochemical research worldwide. Yet, until this unique guide, there were no books offering practical exercises in chemoinformatics methods. Tutorials in Chemoinformatics contains more than 100 exercises in 30 tutorials exploring key topics and methods in the field. It takes an applied approach to the subject with a strong emphasis on problem-solving and computational methodologies. Each tutorial is self-contained and contains exercises for students to work through using a variety of software packages. The majority of the tutorials are divided into three sections devoted to theoretical background, algorithm description and software applications, respectively, with the latter section providing step-by-step software instructions. Throughout, three types of software tools are used: in-house programs developed by the authors, open-source programs and commercial programs which are available for free or at a modest cost to academics. The in-house software and data sets are available on a dedicated companion website. Key topics and methods covered in Tutorials in Chemoinformatics include: -Data curation and standardization -Development and use of chemical databases -Structure encoding by molecular descriptors, text strings and binary fingerprints -The design of diverse and focused libraries -Chemical data analysis and visualization -Structure-property/activity modeling (QSAR/QSPR) -Ensemble modeling approaches, including bagging, boosting, stacking and random subspaces -3D pharmacophores modeling and pharmacological profiling using shape analysis -Protein-ligand docking -Implementation of algorithms in a high-level programming language Tutorials in Chemoinformatics is an ideal supplementary text for advanced undergraduate and graduate courses in chemoinformatics, bioinformatics, computational chemistry, computational biology, medicinal chemistry and biochemistry. It is also a valuable working resource for medicinal chemists, academic researchers and industrial chemists looking to enhance their chemoinformatics skills
Bibliography Includes bibliographical references and index
Notes Print version record and CIP data provided by publisher
Subject Cheminformatics -- Data processing.
Form Electronic book
Author Varnek, Alexandre, editor
LC no. 2017004684
ISBN 1119137977 (Adobe PDF)
1119137985 (ePub)
1119161118
9781119137979 (Adobe PDF)
9781119137986 (ePub)
9781119161110
(cloth)