Title In silico medicinal chemistry : computational methods to support drug design / Nathan Brown

Published [Cambridge] : Royal Society of Chemistry, [2015] ©2016

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Description 1 online resource Series RSC theoretical and computational chemistry series ; 8 RSC theoretical and computational chemistry series ; 8 Contents Cover; In Silico Medicinal Chemistry Computational Methods to Support Drug Design; Preface; Contents; Part 1 Introduction; Chapter 1 -- Introduction; 1.1 Overview; Part 2 Molecular Representations; Chapter 2 -- Chemistry and Graph Theory; 2.1 Overview; 2.2 Graph Theory and Chemistry; 2.3 Graph Theory in Chemistry; 2.4 Mathematical Chemistry and Chemical Graph Theory; 2.5 Summary; References; Chapter 3 -- Structure Representation; 3.1 Overview; 3.2 The Need for Machine-Readable Structure Representations; 3.3 Adjacency Matrix; 3.4 Connection Table; 3.5 Line Notations 3.5.1 WLN: Wiswesser Line Notation3.5.2 SMILES: Simplified Molecular-Input Line-Entry Specification; 3.5.3 InChI: IUPAC International Chemical Identifier; 3.6 Summary; References; Chapter 4 -- Molecular Similarity; 4.1 Overview; 4.2 Molecular Similarity; 4.3 Similar Property Principle; 4.4 Molecular Descriptors; 4.5 Calculation of Molecular Similarity; 4.5.1 Similarity Coefficients; 4.6 Molecular Diversity; 4.7 Summary; References; Part 3 Molecular Descriptors; Chapter 5 -- Molecular Property Descriptors; 5.1 Overview; 5.2 Molecular Weight (MW or MWt) 5.3 Octanol/Water Partition Coefficient (ClogP)5.4 Topological Polar Surface Area (TPSA); 5.5 Hydrogen Bond Acceptors and Donors (HBA and HBD); 5.6 Lipinski's Rule-of-Five; 5.7 Summary; References; Chapter 6 -- Topological Descriptors; 6.1 Overview; 6.2 Topological Indices; 6.2.1 Wiener Index; 6.2.2 Randić Index; 6.2.3 Petitjean Index; 6.2.4 Zagreb Indices; 6.3 Molecular Fingerprints; 6.3.1 Structure-Key Fingerprints; 6.3.2 Hash-Key Fingerprints; 6.3.2.1 Fingal Fingerprints; 6.3.2.2 Morgan Fingerprints; 6.3.3 Ligand-Based Topological Pharmacophores; 6.3.3.1 CATS Vectors 6.3.3.2 Hopfen Fingerprints6.4 Summary; References; Chapter 7 -- Topographical Descriptors; 7.1 Overview; 7.2 Topographic Descriptors; 7.3 Pharmacophores; 7.4 ROCS: Rapid Overlay of Chemical Structures; 7.5 USR: Ultrafast Shape Recognition; 7.6 XED: Cresset Group; 7.7 Conformer Generation and the Conformer Problem; 7.8 Summary; References; Part 4 Statistical Learning; Chapter 8 -- Statistical Learning; 8.1 Overview; 8.2 Statistical Learning; 8.3 Unsupervised Learning; 8.3.1 Overview; 8.3.2 Cluster Analysis; 8.3.3 k-Means Clustering; 8.3.4 Stirling Numbers of the Second Kind 8.3.5 Self-Organising Maps8.3.6 Principal Component Analysis; 8.4 Supervised Learning; 8.4.1 Naïve Bayesian Classification; 8.4.2 Support Vector Machine; 8.4.3 Partial Least Squares; 8.5 Best Modelling Practice; 8.6 Summary; References; Part 5 Modelling Methodologies; Chapter 9 -- Similarity Searching; 9.1 Overview; 9.2 Similar Property Principle; 9.3 Molecular Similarity and Virtual Screening; 9.4 Data Fusion; 9.5 Enrichment; 9.5.1 Lift Plots; 9.5.2 Confusion Matrix; 9.5.3 Receiver Operating Characteristic Curves; 9.5.4 Enrichment Factors; 9.6 Summary; References Chapter 10 -- Bioisosteres and Scaffolds Summary Covering computational tools in drug design using techniques from chemoinformatics, molecular modelling and computational chemistry, this book explores these methodologies and applications of in silico medicinal chemistry. The first part of the book covers molecular representation methods in computing in terms of chemical structure, together with guides on common structure file formats. The second part examines commonly used classes of molecular descriptors. The third part provides a guide to statistical learning methods using chemical structure data, covering topics such as similarity searching, clustering and diversity selection, virtual library design, ligand docking and de novo design. The final part of the book summarises the application of methods to the different stages of drug discovery, from target ID, through hit finding and hit-to-lead, to lead optimisation. This book is a practical introduction to the subject for researchers new to the fields of chemoinformatics, molecular modelling and computational chemistry Notes Includes index English Online resource; title from title details screen (Royal Society of Chemistry, viewed November 19, 2015) Subject Pharmaceutical chemistry -- Data processing Cheminformatics. Drugs -- Design. Pharmaceutical chemistry. Chemistry. Pharmacology. Life sciences. Physical sciences. Computer Simulation Drug Design Computing Methodologies Drug Discovery Investigative Techniques Chemistry, Pharmaceutical Information Science Analytical, Diagnostic and Therapeutic Techniques and Equipment Chemistry Pharmacology Biological Science Disciplines Natural Science Disciplines Disciplines and Occupations Cheminformatics simulation. chemistry. pharmacology. biological sciences. physical sciences. Pre-clinical medicine: basic sciences. Industrial applications of scientific research & technological innovation. SCIENCE -- Applied Sciences. Physical sciences Pharmacology Pharmaceutical chemistry Life sciences Drugs -- Design Chemistry Cheminformatics Pharmaceutical chemistry -- Data processing Form Electronic book Author Royal Society of Chemistry (Great Britain) ISBN 9781782622604 1782622608 9781782627494 1782627499

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