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Computational drug discovery and design

Overview of attention for book
Cover of 'Computational drug discovery and design'

Table of Contents

  1. Altmetric Badge
    Book Overview
  2. Altmetric Badge
    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
Attention for Chapter 20: Linear Interaction Energy: Method and Applications in Drug Design
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Chapter title
Linear Interaction Energy: Method and Applications in Drug Design
Chapter number 20
Book title
Computational Drug Discovery and Design
Published in
Methods in molecular biology, January 2012
DOI 10.1007/978-1-61779-465-0_20
Pubmed ID
Book ISBNs
978-1-61779-464-3, 978-1-61779-465-0
Authors

Hugo Gutiérrez-de-Terán, Johan Åqvist, Gutiérrez-de-Terán, Hugo, Åqvist, Johan

Abstract

A broad range of computational methods exist for the estimation of ligand-protein binding affinities. In this chapter we will provide a guide to the linear interaction energy (LIE) method for binding free energy calculations, focusing on the drug design problem. The method is implemented in combination with molecular dynamics (MD) sampling of relevant conformations of the ligands and complexes under consideration. The detailed procedure for MD sampling is followed by key notes in order to properly analyze such sampling and obtain sufficiently accurate estimations of ligand-binding affinities.

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X Demographics

The data shown below were collected from the profile of 1 X user who shared this research output. Click here to find out more about how the information was compiled.
Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 95 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United Kingdom 4 4%
United States 1 1%
Sri Lanka 1 1%
Italy 1 1%
Unknown 88 93%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 20 21%
Researcher 15 16%
Student > Master 13 14%
Student > Bachelor 9 9%
Student > Doctoral Student 7 7%
Other 12 13%
Unknown 19 20%
Readers by discipline Count As %
Chemistry 26 27%
Agricultural and Biological Sciences 13 14%
Biochemistry, Genetics and Molecular Biology 12 13%
Medicine and Dentistry 6 6%
Pharmacology, Toxicology and Pharmaceutical Science 4 4%
Other 10 11%
Unknown 24 25%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 02 October 2014.
All research outputs
#15,306,972
of 22,765,347 outputs
Outputs from Methods in molecular biology
#5,319
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Outputs of similar age
#163,408
of 244,307 outputs
Outputs of similar age from Methods in molecular biology
#264
of 473 outputs
Altmetric has tracked 22,765,347 research outputs across all sources so far. This one is in the 22nd percentile – i.e., 22% of other outputs scored the same or lower than it.
So far Altmetric has tracked 13,090 research outputs from this source. They receive a mean Attention Score of 3.3. This one is in the 45th percentile – i.e., 45% of its peers scored the same or lower than it.
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We're also able to compare this research output to 473 others from the same source and published within six weeks on either side of this one. This one is in the 34th percentile – i.e., 34% of its contemporaries scored the same or lower than it.