Protein Ligand Interactions and Drug Design 1st editon by Flavio Ballante ISBN 1071612085 978-1071612088

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ISBN 10: 1071612085
ISBN 13: 978-1071612088
Author:  Flavio Ballante 

This detailed book collects modern and established computer-based methods aimed at addressing the drug discovery challenge from disparate perspectives by exploiting information on ligand-protein recognition. Beginning with methods that allow for the exploration of specific areas of chemical space and the designing of virtual libraries, the volume continues with sections on methods based on docking, quantitative models, and molecular dynamics simulations, which are employed for ligand discovery or development, as well as methods exploiting an ensemble of protein structures for the identification of potential protein targets. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Authoritative and cutting-edge, Protein-Ligand Interactions and Drug Design provides detailed practical procedures of solid computer-aided drug design methodologies employed to rationalize and optimize protein-ligand interactions, for experienced researchers and novices alike.

Protein Ligand Interactions and Drug Design 1st Table of contents:

• Investigation of the Click-Chemical Space for Drug Design Using ZINClick
• Molecular Scaffold Hopping via Holistic Molecular Representation
• Biased Docking for Protein-Ligand Pose Prediction
• Binding Mode Prediction and Virtual Screening Applications via Covalent Docking
• Ligand-Receptor and Ligand-DNA Interactions in Drug Design
• Simulation of Ligand Transport in Receptors Using CaverDock
• Negative Image-Based Screening: Rigid Docking Using Cavity Information
• Negative Image-Based Rescoring: Enhancing Docking Screening with Cavity Information
• Fragment-Based Drug Design: Development of Selective HDAC6 Inhibitors
• A Tool for Comparative Binding Energy Analysis to Estimate Drug-Target Residence Time
• Dynamic Docking via Multicanonical Molecular Dynamics: Simulating Complex Formation at the Atomistic Level
• Free Energy Calculations for Protein-Ligand Binding Prediction
• Exploiting Water Dynamics in Pharmacophore Screening
• Markov State Models for Elucidating Ligand Binding Mechanisms
• From Homology Modeling to Hit Identification and Drug Repurposing: A Structure-Based Approach to Discovering Novel Anti-Obesity Compounds
• Multiple Target Drug Design with LigBuilder 3
• Bionoi: A Voronoi Diagram-Based Ligand-Binding Site Representation for Machine Learning Applications
• MDock: A Suite for Molecular Inverse Docking and Target Prediction

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Flavio Ballante,Protein Ligand Interactions,Drug Design