ArticlePLoS computational biology2013
Structure-based function prediction of uncharacterized protein using binding sites comparison.
Article in PLoS computational biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Out-of-distribution generalization enhances protein function annotation for low-homology sequences.Briefings in bioinformatics · 2026Article
- DGSite: A Well-Calibrated Deep Learning Framework for Protein-RNA Binding Site Prediction.ACS omega · 2026Article
- A novel prediction method for protein-DNA binding sites based on protein language model fusion features with SE-connection pyramidal network and ensemble learning.BMC genomics · 2025Article
- Article
- EGPDI: identifying protein-DNA binding sites based on multi-view graph embedding fusion.Briefings in bioinformatics · 2024Article
- EquiPNAS: improved protein-nucleic acid binding site prediction using protein-language-model-informed equivariant deep graph neural networks.Nucleic acids research · 2024Article
- Learning a generalized graph transformer for protein function prediction in dissimilar sequences.GigaScience · 2024Article
- Gene Ontology Capsule GAN: an improved architecture for protein function prediction.PeerJ. Computer science · 2022Article
- CAVIAR: a method for automatic cavity detection, description and decomposition into subcavities.Journal of computer-aided molecular design · 2021Article
- Molecular Dynamics Simulations Reveal Interactions of an IgG1 Antibody With Selected Fc Receptors.Frontiers in chemistry · 2021Article
- DeepRTCP: Predicting ATP-Binding Cassette Transporters Based on 1-Dimensional Convolutional Network.Frontiers in cell and developmental biology · 2020Article
- A benchmark driven guide to binding site comparison: An exhaustive evaluation using tailor-made data sets (ProSPECCTs).PLoS computational biology · 2018Article
- DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier.Bioinformatics (Oxford, England) · 2018Article
- Structure modeling to function prediction of Uncharacterized Human Protein C15orf41.Bioinformation · 2018Article
- Functional Prediction of Hypothetical Transcription Factors ofComputational and structural biotechnology journal · 2018Article
- Discovery of Mycobacterium tuberculosis InhA Inhibitors by Binding Sites Comparison and Ligands Prediction.Journal of medicinal chemistry · 2016Article
- Exploring Human Diseases and Biological Mechanisms by Protein Structure Prediction and Modeling.Advances in experimental medicine and biology · 2016Article
- Role of magnesium ions in the reaction mechanism at the interface between Tm1631 protein and its DNA ligand.Chemistry Central journal · 2016Article
- Modeling enzyme-ligand binding in drug discovery.Journal of cheminformatics · 2015Review
- The emerging era of genomic data integration for analyzing splice isoform function.Trends in genetics : TIG · 2014Review
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A challenge in structural genomics is prediction of the function of uncharacterized proteins. When proteins cannot be related to other proteins of known activity, identification of function based on sequence or structural homology is impossible and in such cases it would be useful to assess structurally conserved binding sites in connection with the protein's function. In this paper, we propose the function of a protein of unknown activity, the Tm1631 protein from Thermotoga maritima, by comparing its predicted binding site to a library containing thousands of candidate structures. The comparison revealed numerous similarities with nucleotide binding sites including specifically, a DNA-binding site of endonuclease IV. We constructed a model of this Tm1631 protein with a DNA-ligand from the newly found similar binding site using ProBiS, and validated this model by molecular dynamics. The interactions predicted by the Tm1631-DNA model corresponded to those known to be important in endonuclease IV-DNA complex model and the corresponding binding free energies, calculated from these models were in close agreement. We thus propose that Tm1631 is a DNA binding enzyme with endonuclease activity that recognizes DNA lesions in which at least two consecutive nucleotides are unpaired. Our approach is general, and can be applied to any protein of unknown function. It might also be useful to guide experimental determination of function of uncharacterized proteins.
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