Bioinformatics and Drug Discovery

1. Front Matter

   Pages i-xi

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2. Translational Bioinformatics in Drug Discovery

   1. Front Matter

      Pages 1-1

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   2. Miniaturized Checkerboard Assays to Measure Antibiotic Interactions

      • Melike Cokol-Cakmak, Murat Cokol

      Pages 3-9

   3. High-Throughput Screening for Drug Combinations

      • Paul Shinn, Lu Chen, Marc Ferrer, Zina Itkin, Carleen Klumpp-Thomas, Crystal McKnight et al.

      Pages 11-35

   4. Post-processing of Large Bioactivity Data

      • Jason Bret Harris

      Pages 37-47

   5. How to Develop a Drug Target Ontology: KNowledge Acquisition and Representation Methodology (KNARM)

      • Hande Küçük McGinty, Ubbo Visser, Stephan Schürer

      Pages 49-69

3. Informatics in Drug Discovery

   1. Front Matter

      Pages 71-71

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   2. A Guide to Dictionary-Based Text Mining

      • Helen V. Cook, Lars Juhl Jensen

      Pages 73-89

   3. Leveraging Big Data to Transform Drug Discovery

      • Benjamin S. Glicksberg, Li Li, Rong Chen, Joel Dudley, Bin Chen

      Pages 91-118

   4. How to Prepare a Compound Collection Prior to Virtual Screening

      • Cristian G. Bologa, Oleg Ursu, Tudor I. Oprea

      Pages 119-138

   5. Building a Quantitative Structure-Property Relationship (QSPR) Model

      • Robert D. Clark, Pankaj R. Daga

      Pages 139-159

   6. Isomeric and Conformational Analysis of Small Drug and Drug-Like Molecules by Ion Mobility-Mass Spectrometry (IM-MS)

      • Shawn T. Phillips, James N. Dodds, Jody C. May, John A. McLean

      Pages 161-178

4. Clinical Research Informatics in Drug Discovery

   1. Front Matter

      Pages 179-179

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   2. A Computational Platform and Guide for Acceleration of Novel Medicines and Personalized Medicine

      • Ioannis N. Melas, Theodore Sakellaropoulos, Junguk Hur, Dimitris Messinis, Ellen Y. Guo, Leonidas G. Alexopoulos et al.

      Pages 181-198

   3. Omics Data Integration and Analysis for Systems Pharmacology

      • Hansaim Lim, Lei Xie

      Pages 199-214

   4. Bioinformatics-Based Tools and Software in Clinical Research: A New Emerging Area

      • Parveen Bansal, Malika Arora, Vikas Gupta, Mukesh Maithani

      Pages 215-230

   5. Text Mining for Drug Discovery

      • Si Zheng, Shazia Dharssi, Meng Wu, Jiao Li, Zhiyong Lu

      Pages 231-252

5. Clinical Informatics in Drug Discovery

   1. Front Matter

      Pages 253-253

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   2. Big Data Cohort Extraction for Personalized Statin Treatment and Machine Learning

      • Terrence J. Adam, Chih-Lin Chi

      Pages 255-272

   3. Drug Signature Detection Based on L1000 Genomic and Proteomic Big Data

      • Wei Chen, Xiaobo Zhou

      Pages 273-286

This third edition volume expands on the previous editions with new topics that cover drug discovery through translational bioinformatics, informatics, clinical research informatics, as well as clinical informatics. The chapters discuss new methods to study target identification, genome analysis, cheminformatics, protein analysis, and text mining. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials, software workflows, reagents and on-line resources, together with step-by-step, readily reproducible laboratory and computational protocols, and tips on troubleshooting and avoiding known pitfalls.



Cutting-edge and thorough, Bioinformatics and Drug Discovery, Third Edition is a valuable resource for anyone interested in drug design, including academicians (biologists, informaticists and data scientists, chemists, and biochemists), clinicians, and pharmaceutical scientists.

• Translational bioinformatics
• Informatics
• Clinical research informatics
• Data mining
• Computational approaches
• drug discovery

• Department of Pathology, University of New Mexico, Albuquerque, USA

  Richard S. Larson

• Department of Internal Medicine, University of New Mexico, Albuquerque, USA

  Tudor I. Oprea

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