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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.

Bioinformatics and Drug Discovery

Preface...

Table of Contents...

Contributing Authors...



Part I Translational Bioinformatics in Drug Discovery



1. Miniaturized Checkerboard Assays to Measure Antibiotic Interactions

Melike Cokol-Cakmak and Murat Cokol



2. High-Throughput Screening for Drug Combinations

Paul Shinn, Lu Chen, Marc Ferrer, Zina Itkin, Carleen Klumpp-Thomas, Crystal McKnight, Sam Michael, Tim Mierzwa, Craig Thomas, Kelli Wilson, Rajarshi Guha



3. Post-Processing of Large Bioactivity Data

Jason Bret Harris



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

Hande Kucuk-McGinty, Ubbo Visser, and Stephan Schurer S.



Part II Informatics in Drug Discovery



5. A Guide to Dictionary-Based Text Mining

Helen V. Cook and Lars Juhl Jensen



6. Leveraging Big Data to Transform Drug Discovery

Benjamin S. Glicksberg, Li Li, Rong Chen, Joel T. Dudley, and Bin Chen



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

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



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

Robert D. Clark and Pankaj R. Daga



9. 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, and John A. McLean



Part III Clinical Research Informatics in Drug Discovery



10. 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, Jane P.F. Bai



11. Omics Data Integration and Analysis for Systems Pharmacology

Hansaim Lim and Lei Xie



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

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



13. Text Mining for Drug Discovery

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



Part IV Clinical Informatics in Drug Discovery



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

Terrence J. Adam and Chih-Lin Chi



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

Wei Chen and Xiaobo Zhou



16. Drug Effect Prediction by Integrating L1000 Genomic and Proteomic Big Data

Wei Chen and Xiaobo Zhou



17. A Bayesian Network Approach to Disease Subtype Discovery

Mei-Sing Ong