ArticleJournal of cheminformatics2019
Binding mode information improves fragment docking.
Article in Journal of cheminformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 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
9 citing papers in PubMed.
- Predicting fragment binding modes using customized Lennard-Jones potentials in short molecular dynamics simulations.Computational and structural biotechnology journal · 2025Article
- Molecular Docking in Drug Discovery: Techniques, Applications, and Advancements.Current medicinal chemistry · 2025Review
- CSAlign and CSAlign-Dock: Structure alignment of ligands considering full flexibility and application to protein-ligand docking.Computational and structural biotechnology journal · 2023Article
- In vitro activity of celastrol in combination with thymol against carbapenem-resistant Klebsiella pneumoniae isolates.The Journal of antibiotics · 2022Article
- Re-Exploring the Ability of Common Docking Programs to Correctly Reproduce the Binding Modes of Non-Covalent Inhibitors of SARS-CoV-2 Protease MPharmaceuticals (Basel, Switzerland) · 2022Article
- Biased Docking for Protein-Ligand Pose Prediction.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Merging Ligand-Based and Structure-Based Methods in Drug Discovery: An Overview of Combined Virtual Screening Approaches.Molecules (Basel, Switzerland) · 2020Review
- Review
- Local Interaction Density (LID), a Fast and Efficient Tool to Prioritize Docking Poses.Molecules (Basel, Switzerland) · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Docking is commonly used in drug discovery to predict how ligand binds to protein target. Best programs are generally able to generate a correct solution, yet often fail to identify it. In the case of drug-like molecules, the correct and incorrect poses can be sorted by similarity to the crystallographic structure of the protein in complex with reference ligands. Fragments are particularly sensitive to scoring problems because they are weak ligands which form few interactions with protein. In the present study, we assessed the utility of binding mode information in fragment pose prediction. We compared three approaches: interaction fingerprints, 3D-matching of interaction patterns and 3D-matching of shapes. We prepared a test set composed of high-quality structures of the Protein Data Bank. We generated and evaluated the docking poses of 586 fragment/protein complexes. We observed that the best approach is twice as accurate as the native scoring function, and that post-processing is less effective for smaller fragments. Interestingly, fragments and drug-like molecules both proved to be useful references. In the discussion, we suggest the best conditions for a successful pose prediction with the three approaches.
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.