ArticleJournal of chemical information and modeling2020
Exploring Ligand Stability in Protein Crystal Structures Using Binding Pose Metadynamics.
Article in Journal of chemical information and modeling, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 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
63 citing papers in PubMed.
- Integrative gene target mapping, RNA sequencing, in silico molecular docking, ADMET profiling and molecular dynamics simulation study of marine derived molecules for type 1 diabetes mellitus.Molecular diversity · 2026Article
- Integrated Molecular Docking and Molecular Dynamics Approaches Reveal Potential Antimicrobial Metabolites from Echinoderms,Biology · 2026Article
- QSAR-ML- and Metadynamics-Guided Design of Symmetrical Bis-Indanones to Overcome Mutational Anchor Loss in Acetylcholinesterase.Pharmaceuticals (Basel, Switzerland) · 2026Article
- Harnessing the structural determinants amenable for polypharmacological behavior of 7D against Sirt1 and CXCR3.iScience · 2026Article
- Disrupting virulence: in silico discovery of MexL inhibitors to block pyocyanin biosynthesis in Pseudomonas aeruginosa.Archives of microbiology · 2026Article
- Computational Analysis of ELOVL6 Structure and Inhibition for Rational Drug Design.Journal of chemical information and modeling · 2026Article
- Dynamic stability-driven machine learning improves binding pose identification on human serum albumin.Journal of computer-aided molecular design · 2026Article
- The identification of potent nonopioid analgesics and their potential for perioperative use.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Mechanistic inhibition of FtsZ-driven bacterial cytokinesis by natural products: an integrated machine learning and advanced drug discovery approach.Molecular diversity · 2026Article
- Clove Essential Oil as an Antifungal Agent and Putative Dual-Action Antifungal Mechanism: Experimental Validation and Computational Insights into Orthosteric and Allosteric Modulation of Chitin Synthase I inMolecules (Basel, Switzerland) · 2026Article
- Structural and Dynamics Analyses of β-Lactam Inhibition ofACS chemical biology · 2026Article
- Highly enantioselective reduction of benzophenones by engineered Geotrichum candidum alcohol dehydrogenase.Applied microbiology and biotechnology · 2026Article
- In silico pharmacological analysis of Tinospora cordifolia compounds targeting African swine fever virus B175L.PloS one · 2026Article
- Repurposing of lansoprazole and nitazoxanide as NR2F2 inhibitors in the gastric cancer cell line GCIY: computational insights and siRNA-mediatedFrontiers in chemistry · 2026Article
- Development of substituted 2-(4-(sulfonyl)piperazin-1-yl)quinazoline molecular hybrids as a new class of antimalarials.RSC advances · 2025Article
- Molecular Docking and Dynamics Simulations Reveal the Antidiabetic Potential of a Novel Fucoxanthin Derivative fromMarine drugs · 2025Article
- Decoding SP-D and glycan binding mechanisms using a novel computational workflow.Biophysical journal · 2025Article
- Safe delivery of a highly toxic anthracycline derivative through liposomal nanoformulation achieves complete cancer regression.Molecular cancer · 2025Article
- Computational insights into harmala alkaloids as novel antimalarial candidates against Plasmodium falciparum.Scientific reports · 2025Article
- Discovery and Characterization of Uracil Derivatives Targeting the Set-and-Ring Domain of UHRF1.Journal of chemical information and modeling · 2025Article
3 more citing papers are in PubMed but not listed here.
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
No grant is acknowledged in the PubMed record.
Abstract
Identification of correct protein-ligand binding poses is important in structure-based drug design and crucial for the evaluation of protein-ligand binding affinity. Protein-ligand coordinates are commonly obtained from crystallography experiments that provide a static model of an ensemble of conformations. Binding pose metadynamics (BPMD) is an enhanced sampling method that allows for an efficient assessment of ligand stability in solution. Ligand poses that are unstable under the bias of the metadynamics simulation are expected to be infrequently occupied in the energy landscape, thus making minimal contributions to the binding affinity. Here, the robustness of the method is studied using crystal structures with ligands known to be incorrectly modeled, as well as 63 structurally diverse crystal structures with ligand fit to electron density from the Twilight database. Results show that BPMD can successfully differentiate compounds whose binding pose is not supported by the electron density from those with well-defined electron density.
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.