ArticleBiochemistry2015
Covalent docking predicts substrates for haloalkanoate dehalogenase superfamily phosphatases.
Article in Biochemistry, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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Who cites it
11 citing papers in PubMed, 27 citations in OpenAlex.
- Review
- Biosynthesis, Regulation, and Biotechnological Production Strategies of Riboflavin (Vitamin BPharmaceuticals (Basel, Switzerland) · 2026Review
- Structure-based rational design of covalent probes.Communications chemistry · 2025Review
- Covalent docking in CDOCKER.Journal of computer-aided molecular design · 2022Article
- Production of riboflavin and related cofactors by biotechnological processes.Microbial cell factories · 2020Review
- High-Efficiency Secretion and Directed Evolution of Chitinase BcChiA1 inFrontiers in bioengineering and biotechnology · 2020Article
- Overcoming insecticide resistance through computational inhibitor design.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Systematic Studies on the Protocol and Criteria for Selecting a Covalent Docking Tool.Molecules (Basel, Switzerland) · 2019Article
- Crius: A novel fragment-based algorithm of de novo substrate prediction for enzymes.Protein science : a publication of the Protein Society · 2018Article
- Recent Advances and Applications of Molecular Docking to G Protein-Coupled Receptors.Molecules (Basel, Switzerland) · 2017Review
- Docking Screens for Novel Ligands Conferring New Biology.Journal of medicinal chemistry · 2016Review
Corrections and comments
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Authors and funding
11 authors at 5 institutions in 2 countries.
Funding
Abstract
Enzyme function prediction remains an important open problem. Though structure-based modeling, such as metabolite docking, can identify substrates of some enzymes, it is ill-suited to reactions that progress through a covalent intermediate. Here we investigated the ability of covalent docking to identify substrates that pass through such a covalent intermediate, focusing particularly on the haloalkanoate dehalogenase superfamily. In retrospective assessments, covalent docking recapitulated substrate binding modes of known cocrystal structures and identified experimental substrates from a set of putative phosphorylated metabolites. In comparison, noncovalent docking of high-energy intermediates yielded nonproductive poses. In prospective predictions against seven enzymes, a substrate was identified for five. For one of those cases, a covalent docking prediction, confirmed by empirical screening, and combined with genomic context analysis, suggested the identity of the enzyme that catalyzes the orphan phosphatase reaction in the riboflavin biosynthetic pathway of Bacteroides.
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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.