Computational Drug Discovery and Design: (1762 Methods in Molecular Biology)

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.

Table of Contents:
Computer-Aided Drug Design – An Overview.- Prediction of Human Drug Targets and their Interactions Using Machine Learning Methods: Current and Future Perspectives.- Practices in Molecular Docking and Structure-based Virtual Screening.- Phylogenetic and Conservation Based Approaches to Predict Protein Functional Sites.- De novo design of Ligands using Computational Methods.- Molecular Dynamics Simulation and the Prediction of Druggable Binding Sites.- Virtual Ligand Screening using PL-PatchSurfer2, a Molecular Surface-based Protein-ligand Docking Method.- Fragment Based Ligand Designing.- Molecular Dynamics as a Tool for Virtual Ligand Screening.- Building Molecular Interaction Networks from Microarray Data for Drug Target Screening.- Absolute Alchemical Free Energy Calculations for Ligand Binding.- Evaluation of Protein-ligand Docking by Cyscore.- Molecular Dynamics Simulations of Protein-drug Complexes:  A Computational Protocol for Investigating the Interactions of Small-Molecule Therapeutics with Biological Targets and Biosensors.- Prediction and Optimization of Pharmacokinetic and Toxicity Properties of the Ligand.- Protein-protein Docking in Drug Design and Discovery.- Automated Inference of Chemical Discriminants of Biological Activity.- Computational Exploration of Conformational Transitions in Protein Drug Targets.- Applications of the NRGsuite and the Molecular Docking Software FlexAID in Computational Drug Discovery and Design.- Calculation of Thermodynamic Properties of Bound Water Molecules.- Enhanced Molecular Dynamics Methods Applied to Drug Design Projects.- AGGRESCAN3D: Towards the Prediction of the Aggregation Propensities of Protein Structures.- Computational Analysis of Solvent Inclusion in Docking Studies of Protein-glycosaminoglycan Systems.- Understanding G Protein-Coupled Receptor Allostery via Molecular Dynamics Simulations: Implications for Drug Discovery.- Identification of Potential Microrna Biomarkers by Meta-analysis.