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Protein-Ligand Interactions and Drug Design
Title
Protein-Ligand Interactions and Drug Design [electronic resource] / edited by Flavio Ballante.
ISBN
9781071612095
Edition
1st ed. 2021.
Publication
New York, NY : Springer US : Imprint: Humana, 2021.
Physical Description
1 online resource (XV, 327 p.) 107 illus., 81 illus. in color.
Local Notes
Access is available to the Yale community.
Access and use
Access restricted by licensing agreement.
Summary
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.
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Springer protocols (Series)
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Format
Books / Online
Language
English
Added to Catalog
April 12, 2021
Series
Methods in Molecular Biology, 2266
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 by Covalent Docking
Ligand-Receptor, Ligand-DNA Interactions and Drug Design
Simulation of Ligand Transport in Receptors Using CaverDock
Negative Image-Based Screening: Rigid Docking Using Cavity Information
Negative Image-Based Rescoring: Using Cavity Information to Improve Docking Screening
Fragment-Based Drug Design of Selective HDAC6 Inhibitors
A Protocol to Use Comparative Binding Energy Analysis to Estimate Drug-Target Residence Time
Dynamic Docking Using Multicanonical Molecular Dynamics: Simulating Complex Formation at the Atomistic Level
Free Energy Calculations for Protein-Ligand Binding Prediction
Exploiting Water Dynamics for Pharmacophore Screening
Markov State Models to Elucidate Ligand Binding Mechanism
From Homology Modeling to the Hit Identification and Drug Repurposing: A Structure-Based Approach in the Discovery of Novel Potential Anti-Obesity Compounds
Multiple Target Drug Design Using LigBuilder 3
Bionoi: A Voronoi Diagram-Based Representation of Ligand-Binding Sites in Proteins for Machine Learning Applications
MDock: A Suite for Molecular Inverse Docking and Target Prediction.
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