ArticleJournal of chemical information and modeling2012
Utilizing experimental data for reducing ensemble size in flexible-protein docking.
Article in Journal of chemical information and modeling, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- PopShift: A Thermodynamically Sound Approach to Estimate Binding Free Energies by Accounting for Ligand-Induced Population Shifts from a Ligand-Free Markov State Model.Journal of chemical theory and computation · 2024Article
- On the Rapid Calculation of Binding Affinities for Antigen and Antibody Design and Affinity Maturation Simulations.Antibodies (Basel, Switzerland) · 2022Article
- Extensive Sampling of Molecular Dynamics Simulations to Identify Reliable Protein Structures for Optimized Virtual Screening Studies: The Case of the hTRPM8 Channel.International journal of molecular sciences · 2022Article
- Ensemble learning from ensemble docking: revisiting the optimum ensemble size problem.Scientific reports · 2022Article
- Improving Structure-Based Virtual Screening with Ensemble Docking and Machine Learning.Journal of chemical information and modeling · 2021Article
- Targeting the C-Terminal Domain Small Phosphatase 1.Life (Basel, Switzerland) · 2020Review
- ALADDIN: Docking Approach Augmented by Machine Learning for Protein Structure Selection Yields Superior Virtual Screening Performance.Molecular informatics · 2020Article
- Efficient flexible backbone protein-protein docking for challenging targets.Bioinformatics (Oxford, England) · 2018Article
- Efficiency of Stratification for Ensemble Docking Using Reduced Ensembles.Journal of chemical information and modeling · 2018Article
- A cross docking pipeline for improving pose prediction and virtual screening performance.Journal of computer-aided molecular design · 2018Article
- Enhancing Virtual Screening Performance of Protein Kinases with Molecular Dynamics Simulations.Journal of chemical information and modeling · 2016Article
- Knowledge-Based Methods To Train and Optimize Virtual Screening Ensembles.Journal of chemical information and modeling · 2016Article
- Enrichment of chemical libraries docked to protein conformational ensembles and application to aldehyde dehydrogenase 2.Journal of chemical information and modeling · 2014Article
- Induced fit docking, and the use of QM/MM methods in docking.Drug discovery today. Technologies · 2013Review
- Highly predictive ligand-based pharmacophore and homology models of ABHD6.Chemical biology & drug design · 2013Article
- Rational prediction with molecular dynamics for hit identification.Current topics in medicinal chemistry · 2012Review
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Authors and funding
2 authors.
Funding
Abstract
Efficient and sufficient incorporation of protein flexibility into docking is still a challenging task. Docking to an ensemble of protein structures has proven its utility for docking, but using a large ensemble of structures can reduce the efficiency of docking and can increase the number of false positives in virtual screening. In this paper, we describe the application of our new methodology, Limoc, to generate an ensemble of holo-like protein structures in combination with the relaxed complex scheme (RCS), to virtual screening. We describe different schemes to reduce the ensemble of protein structures to increase efficiency and enrichment quality. Utilizing experimental knowledge about actives for a target protein allows the reduction of ensemble members to a minimum of three protein structures, increasing enrichment quality and efficiency simultaneously.
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