ArticleJournal of chemical information and modeling2009
Consistent improvement of cross-docking results using binding site ensembles generated with elastic network normal modes.
Article in Journal of chemical information and modeling, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
39 citing papers in PubMed.
- Open-Source Molecular Docking and AI-Augmented Structure-Based Drug Design: Current Workflows, Challenges, and Opportunities.International journal of molecular sciences · 2026Review
- A Computationally Efficient Method to Generate Plausible Conformers for Ensemble Docking and Binding Free Energy Calculations.Journal of chemical information and modeling · 2025Article
- Multi-Targeted Approaches and Drug Repurposing Reveal Possible SARS-CoV-2 Inhibitors.Vaccines · 2021Article
- Article
- Subtle Chemical Changes Cross the Boundary between Agonist and Antagonist: New AJournal of medicinal chemistry · 2021Article
- A unique ligand-steered strategy for CC chemokine receptor 2 homology modeling to facilitate structure-based virtual screening.Chemical biology & drug design · 2021Article
- OMN6 a novel bioengineered peptide for the treatment of multidrug resistant Gram negative bacteria.Scientific reports · 2021Article
- Using collections of structural models to predict changes of binding affinity caused by mutations in protein-protein interactions.Protein science : a publication of the Protein Society · 2020Article
- Druggability Simulations and X-Ray Crystallography Reveal a Ligand-Binding Site in the GluA3 AMPA Receptor N-Terminal Domain.Structure (London, England : 1993) · 2019Article
- Article
- ENCoM server: exploring protein conformational space and the effect of mutations on protein function and stability.Nucleic acids research · 2015Article
- The anisotropic network model web server at 2015 (ANM 2.0).Bioinformatics (Oxford, England) · 2015Article
- SEABED: Small molEcule activity scanner weB servicE baseD.Bioinformatics (Oxford, England) · 2015Article
- Structure-based virtual screening of the nociceptin receptor: hybrid docking and shape-based approaches for improved hit identification.Journal of chemical information and modeling · 2014Article
- Molecular dynamics, dynamic site mapping, and highthroughput virtual screening on leptin and the Ob receptor as anti-obesity target.Journal of molecular modeling · 2014Article
- Receptor-ligand molecular docking.Biophysical reviews · 2014Review
- Docking to multiple pockets or ligand fields for screening, activity prediction and scaffold hopping.Future medicinal chemistry · 2014Article
- In silico mechanistic profiling to probe small molecule binding to sulfotransferases.PloS one · 2013Article
- Pocket-based drug design: exploring pocket space.The AAPS journal · 2013Review
- Consensus Induced Fit Docking (cIFD): methodology, validation, and application to the discovery of novel Crm1 inhibitors.Journal of computer-aided molecular design · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
The representation of protein flexibility is still a challenge for the state-of-the-art flexible ligand docking protocols. In this article, we use a large and diverse benchmark to prove that is possible to improve consistently the cross-docking performance against a single receptor conformation, using an equilibrium ensemble of binding site conformers. The benchmark contained 28 proteins, and our method predicted the top-ranked near native ligand poses 20% more efficiently than using a single receptor. The multiple conformations were derived from the collective variable space defined by all heavy-atom elastic network normal modes, including backbone and side chains. We have found that the binding site displacements for best positioning of the ligand seem rather independent from the global collective motions of the protein. We also found that the number of binding site conformations needed to represent nonredundant flexibility was < 100. The ensemble of receptor conformations can be generated at our Web site at http://abagyan.scripps.edu/MRC.
Indexed as
Identifiers
What OpenQuestion holds
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.