ArticleJournal of chemical information and modeling2011
Using free energy of binding calculations to improve the accuracy of virtual screening predictions.
Article in Journal of chemical information and modeling, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Computational Analysis of Antimicrobial Peptides Targeting Agglutinin-Like Protein 3 (Als3) and β-Glucan Synthase in Denture-Associated Candidiasis.International dental journal · 2026Article
- Virtual screening: hope, hype, and the fine line in between.Expert opinion on drug discovery · 2025Review
- Structure-threshold relationship in food aroma molecules: Insights from S-curve method, molecular docking, and dynamics simulations.Current research in food science · 2025Article
- Synthesis, molecular docking, and binding Gibbs free energy calculation of β-nitrostyrene derivatives: Potential inhibitors of SARS-CoV-2 3CL protease.Journal of molecular structure · 2023Article
- Free Energy Calculations Using the Movable Type Method with Molecular Dynamics Driven Protein-Ligand Sampling.Journal of chemical information and modeling · 2022Article
- The anti-inflammatory potential of cefazolin as common gamma chain cytokine inhibitor.Scientific reports · 2020Article
- PIP3-binding proteins promote age-dependent protein aggregation and limit survival in C. elegans.Oncotarget · 2016Article
- Structure-based virtual screening for drug discovery: principles, applications and recent advances.Current topics in medicinal chemistry · 2014Review
- Current progress in Structure-Based Rational Drug Design marks a new mindset in drug discovery.Computational and structural biotechnology journal · 2013Review
- Cloud infrastructures for in silico drug discovery: economic and practical aspects.BioMed research international · 2013Article
- Perspective: Alchemical free energy calculations for drug discovery.The Journal of chemical physics · 2012Article
- Application of binding free energy calculations to prediction of binding modes and affinities of MDM2 and MDMX inhibitors.Journal of chemical information and modeling · 2012Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Virtual screening of small molecule databases against macromolecular targets was used to identify binding ligands and predict their lowest energy bound conformation (i.e., pose). AutoDock4-generated poses were rescored using mean-field pathway decoupling free energy of binding calculations and evaluated if these calculations improved virtual screening discrimination between bound and nonbound ligands. Two small molecule databases were used to evaluate the effectiveness of the rescoring algorithm in correctly identifying binders of L99A T4 lysozyme. Self-dock calculations of a database containing compounds with known binding free energies and cocrystal structures largely reproduced experimental measurements, although the mean difference between calculated and experimental binding free energies increased as the predicted bound poses diverged from the experimental poses. In addition, free energy rescoring was more accurate than AutoDock4 scores in discriminating between known binders and nonbinders, suggesting free energy rescoring could be a useful approach to reduce false positive predictions in virtual screening experiments.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.