Description
This volume details methods and techniques for identification of drug targets, binding sites prediction, high-throughput virtual screening,and prediction of pharmacokinetic properties using computer based methodologies. Chapters guide readers through techniques of the available computational tools, developing prediction models for drug target prediction and de novo design of ligands, structure based drug designing, fragment-based drug designing, molecular docking, and scoring functions for assessing protein-ligand docking protocols. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials, step-by-step, readily reproducible protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Computational Drug Discovery and Design aims to provide protocols for the use of bioinformatics tools in drug discovery and design. 1. Computer-Aided Drug Design – An Overview Alan Talevi 2. Prediction of Human Drug Targets and their Interactions Using Machine Learning Methods: Current and Future Perspectives Abhigyan Nath, Priyanka Kumari, and Radha Chaube 3. Practices in Molecular Docking and Structure-based Virtual Screening Ricardo N. dos Santos, Leonardo G. Ferreira, and Adriano D. Andricopulo 4. Phylogenetic and Conservation Based Approaches to Predict Protein Functional Sites Heval Atas, Nurcan Tuncbag, and Tunca Dogan 5. De novo design of Ligands using Computational Methods Venkatesan Suryanarayanan, Umesh Panwar, Ishwar Chandra, and Sanjeev Kumar Singh 6. Molecular Dynamics Simulation and the Prediction of Druggable Binding Sites Tianhua Feng and Khaled Barakat 7. Virtual Ligand Screening using PL-PatchSurfer2, a Molecular Surface-based Protein-ligand Docking Method Woong-Hee Shin and Daisuke Kihara 8. Fragment Based Ligand Designing Shashank P. Katiyar, Vidhi Malik, Anjani Kumari, Kamya Singh,and Durai Sundar 9. Molecular Dynamics as a Tool for Virtual Ligand Screening Grgory Menchon, Laurent Maveyraud, and Georges Czaplicki 10. Building Molecular Interaction Networks from Microarray Data for Drug Target Screening Sze Chung Yuen, Hongmei Zhu, and Siu-wai Leung 11. Absolute Alchemical Free Energy Calculations for Ligand Binding Matteo Aldeghi, Joseph P. Bluck, and Philip C. Biggin 12. Evaluation of Protein-ligand Docking by Cyscore Yang Cao, Wentao Dai, and Zhichao Miao 13. Molecular Dynamics Simulations of Protein-drug Complexes: A Computational Protocol for Investigating the Interactions of Small-Molecule Therapeutics with Biological Targets and Biosensors Jodi A. Hadden and Juan R. Perilla 14. Prediction and Optimization of Pharmacokinetic and Toxicity Properties of the Ligand Douglas E. V. Pires, Lisa M. Kaminskas, and David B. Ascher 15. Protein-protein Docking in Drug Design and Discovery Agnieszka A. Kaczor, Damian Bartuzi, Tomasz Maciej Stepniewski, and Dariusz Matosiuk, and Jana Selent 16. Automated Inference of Chemical Discriminants of Biological Activity Sebastian Raschka, Anne M. Scott, Mar Huertas, Weiming Li, and Leslie A. Kuhn 17. Computational Exploration of Conformational Transitions in Protein Drug Targets Benjamin P. Cossins and Alastair D. G. Lawson, Jiye Shi 18. Applications of the NRGsuite and the Molecular Docking Software FlexAID in Computational Drug Discovery and Design Louis-Philippe Morency, Francis Gaudreault, and Rafael Najmanovich 19. Calculation of Thermodynamic Properties of Bound Water Molecules Ying Yang, Amr Abdallah, and Markus A. Lill 20. Enhanced Molecular Dynamics Methods Applied to Drug Design Projects Sonia Ziada, Abdennour Braka, Julien Diharce, Samia Aci-Sche, and Pascal Bonnet 21. AGGRESCAN3D: Towards the Prediction of the Aggregation Propensities of Protein Structures Jordi Pujols, Samuel Pea-Daz, and Salvador Ventura 22. Computational Analysis of Solvent Inclusion in Docking Studies of Protein-glycosaminoglycan Systems Sergey A. Samsonov 23. Understanding G Protein-Coupled Receptor Allostery via Molecular Dynamics Simulations: Implications for Drug Discovery Shaherin Basith, Yoonji Lee, and Sun Choi 24. Identification of Potential Microrna Biomarkers by Meta-analysis Hongmei Zhu and Siu-wai Leung
