ArticleJournal of chemical information and modeling2009
Molecular docking screens using comparative models of proteins.
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 71 papers.
What it found
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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.
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Who cites it
71 citing papers in PubMed.
- KASSPer: kinase active site structure prediction using protein and ligand language models and its application to virtual screening.Bioinformatics (Oxford, England) · 2026Article
- PL-PatchSurfer3: improved structure-based virtual screening for structure variation using 3D Zernike descriptors.Journal of cheminformatics · 2026Article
- Solvent-Site Prediction for Fragment Docking and Its Implication on Fragment-Based Drug Discovery.Journal of chemical information and modeling · 2025Article
- Improving docking and virtual screening performance using AlphaFold2 multi-state modeling for kinases.Scientific reports · 2024Article
- Protein language models are performant in structure-free virtual screening.Briefings in bioinformatics · 2024Article
- A comprehensive exploration of the druggable conformational space of protein kinases using AI-predicted structures.PLoS computational biology · 2024Article
- Targeting SLC transporters: small molecules as modulators and therapeutic opportunities.Trends in biochemical sciences · 2023Review
- Evaluation of AlphaFold2 structures as docking targets.Protein science : a publication of the Protein Society · 2023Article
- Structural Elucidation of Rift Valley Fever Virus L Protein towards the Discovery of Its Potential Inhibitors.Pharmaceuticals (Basel, Switzerland) · 2022Article
- Ferric quinate (QPLEX) interacts with the major outer membrane protein (MOMP) ofComputational and structural biotechnology journal · 2022Article
- Structure-based virtual screening of CYP1A1 inhibitors: towards rapid tier-one assessment of potential developmental toxicants.Archives of toxicology · 2021Article
- Molecular docking-aided identification of small molecule inhibitors targeting β-catenin-TCF4 interaction.iScience · 2021Article
- Virtual screening of potentially endocrine-disrupting chemicals against nuclear receptors and its application to identify PPARγ-bound fatty acids.Archives of toxicology · 2021Article
- Performance of virtual screening against GPCR homology models: Impact of template selection and treatment of binding site plasticity.PLoS computational biology · 2020Article
- Perspectives towards antiviral drug discovery against Ebola virus.Journal of medical virology · 2019Review
- Article
- Modeling the binding of diverse ligands within the Ah receptor ligand binding domain.Scientific reports · 2019Article
- Ligity: A Non-Superpositional, Knowledge-Based Approach to Virtual Screening.Journal of chemical information and modeling · 2019Article
- In silico structural elucidation of RNA-dependent RNA polymerase towards the identification of potential Crimean-Congo Hemorrhagic Fever Virus inhibitors.Scientific reports · 2019Article
- Integrated computational and Drosophila cancer model platform captures previously unappreciated chemicals perturbing a kinase network.PLoS computational biology · 2019Article
11 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Two orders of magnitude more protein sequences can be modeled by comparative modeling than have been determined by X-ray crystallography and NMR spectroscopy. Investigators have nevertheless been cautious about using comparative models for ligand discovery because of concerns about model errors. We suggest how to exploit comparative models for molecular screens, based on docking against a wide range of crystallographic structures and comparative models with known ligands. To account for the variation in the ligand-binding pocket as it binds different ligands, we calculate "consensus" enrichment by ranking each library compound by its best docking score against all available comparative models and/or modeling templates. For the majority of the targets, the consensus enrichment for multiple models was better than or comparable to that of the holo and apo X-ray structures. Even for single models, the models are significantly more enriching than the template structure if the template is paralogous and shares more than 25% sequence identity with the target.
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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.