Computational drug discovery and design

Table of Contents

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   Book Overview
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   Chapter 1 A Molecular Dynamics Ensemble-Based Approach for the Mapping of Druggable Binding Sites
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   Chapter 2 Analysis of Protein Binding Sites by Computational Solvent Mapping
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   Chapter 3 Evolutionary Trace for Prediction and Redesign of Protein Functional Sites
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   Chapter 4 Information Entropic Functions for Molecular Descriptor Profiling
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   Chapter 5 Expanding the conformational selection paradigm in protein-ligand docking.
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   Chapter 6 Flexibility Analysis of Biomacromolecules with Application to Computer-Aided Drug Design
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   Chapter 7 On the Use of Molecular Dynamics Receptor Conformations for Virtual Screening
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   Chapter 8 Virtual Ligand Screening Against Comparative Protein Structure Models
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    Chapter 9 AMMOS Software: Method and Application
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    Chapter 10 Rosetta Ligand Docking with Flexible XML Protocols.
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    Chapter 11 Normal Mode-Based Approaches in Receptor Ensemble Docking
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    Chapter 12 Application of Conformational Clustering in Protein–Ligand Docking
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    Chapter 13 How to Benchmark Methods for Structure-Based Virtual Screening of Large Compound Libraries
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    Chapter 14 AGGRESCAN: Method, Application, and Perspectives for Drug Design
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    Chapter 15 ATTRACT and PTOOLS: Open Source Programs for Protein–Protein Docking
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    Chapter 16 Prediction of Interacting Protein Residues Using Sequence and Structure Data
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    Chapter 17 MM-GB/SA Rescoring of Docking Poses
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    Chapter 18 A Case Study of Scoring and Rescoring in Peptide Docking
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    Chapter 19 The Solvated Interaction Energy Method for Scoring Binding Affinities
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    Chapter 20 Linear Interaction Energy: Method and Applications in Drug Design
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    Chapter 21 Computational Drug Discovery and Design
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    Chapter 22 Explicit Treatment of Water Molecules in Data-Driven Protein–Protein Docking: The Solvated HADDOCKing Approach
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    Chapter 23 Protein–Water Interactions in MD Simulations: POPS/POPSCOMP Solvent Accessibility Analysis, Solvation Forces and Hydration Sites
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    Chapter 24 Computing the Thermodynamic Contributions of Interfacial Water
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    Chapter 25 Assignment of Protonation States in Proteins and Ligands: Combining pKa Prediction with Hydrogen Bonding Network Optimization
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    Chapter 26 Computational Drug Discovery and Design
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    Chapter 27 Independent-Trajectory Thermodynamic Integration: A Practical Guide to Protein-Drug Binding Free Energy Calculations Using Distributed Computing
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    Chapter 28 Free Energy Calculations from One-Step Perturbations
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    Chapter 29 Using Metadynamics and Path Collective Variables to Study Ligand Binding and Induced Conformational Transitions
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    Chapter 30 Accelerated Molecular Dynamics in Computational Drug Design
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    Chapter 31 Computational Drug Discovery and Design
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    Chapter 32 Decomposing the Energetic Impact of Drug-Resistant Mutations: The Example of HIV-1 Protease–DRV Binding
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    Chapter 33 Guide to Virtual Screening: Application to the Akt Phosphatase PHLPP.
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    Chapter 34 Molecular-Level Simulation of Pandemic Influenza Glycoproteins
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    Chapter 35 Homology Modeling of Cannabinoid Receptors: Discovery of Cannabinoid Analogues for Therapeutic Use
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    Chapter 36 High-Throughput Virtual Screening Lead to Discovery of Non-Peptidic Inhibitors of West Nile Virus NS3 Protease