Main 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.

Contents:

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

Gregory 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-Seche, and Pascal Bonnet

21. AGGRESCAN3D: Towards the Prediction of the Aggregation Propensities of Protein Structures

Jordi Pujols, Samuel Pena-Diaz, 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