ArticleNucleic acids research2013
DBSI: DNA-binding site identifier.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 32 citations in OpenAlex.
- Twenty years of advances in prediction of nucleic acid-binding residues in protein sequences.Briefings in bioinformatics · 2024Review
- Opinion: Protein folds vs. protein folding: Differing questions, different challenges.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- m5CPred-SVM: a novel method for predicting m5C sites of RNA.BMC bioinformatics · 2020Article
- iPNHOT: a knowledge-based approach for identifying protein-nucleic acid interaction hot spots.BMC bioinformatics · 2020Article
- Multiple protein-DNA interfaces unravelled by evolutionary information, physico-chemical and geometrical properties.PLoS computational biology · 2020Article
- PredPSD: A Gradient Tree Boosting Approach for Single-Stranded and Double-Stranded DNA Binding Protein Prediction.Molecules (Basel, Switzerland) · 2019Article
- RNAm5CPred: Prediction of RNA 5-Methylcytosine Sites Based on Three Different Kinds of Nucleotide Composition.Molecular therapy. Nucleic acids · 2019Article
- PseUI: Pseudouridine sites identification based on RNA sequence information.BMC bioinformatics · 2018Article
- Electrostatic Interactions in Protein Structure, Folding, Binding, and Condensation.Chemical reviews · 2018Review
- PredT4SE-Stack: Prediction of Bacterial Type IV Secreted Effectors From Protein Sequences Using a Stacked Ensemble Method.Frontiers in microbiology · 2018Article
- Analysis and prediction of single-stranded and double-stranded DNA binding proteins based on protein sequences.BMC bioinformatics · 2017Article
- Predicting hot spots in protein interfaces based on protrusion index, pseudo hydrophobicity and electron-ion interaction pseudopotential features.Oncotarget · 2016Article
- SNBRFinder: A Sequence-Based Hybrid Algorithm for Enhanced Prediction of Nucleic Acid-Binding Residues.PloS one · 2015Article
- Mitochondrial COQ9 is a lipid-binding protein that associates with COQ7 to enable coenzyme Q biosynthesis.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Analysis and classification of DNA-binding sites in single-stranded and double-stranded DNA-binding proteins using protein information.IET systems biology · 2014Article
- Visualizing Validation of Protein Surface Classifiers.Computer graphics forum : journal of the European Association for Computer Graphics · 2014Article
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Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In this study, we present the DNA-Binding Site Identifier (DBSI), a new structure-based method for predicting protein interaction sites for DNA binding. DBSI was trained and validated on a data set of 263 proteins (TRAIN-263), tested on an independent set of protein-DNA complexes (TEST-206) and data sets of 29 unbound (APO-29) and 30 bound (HOLO-30) protein structures distinct from the training data. We computed 480 candidate features for identifying protein residues that bind DNA, including new features that capture the electrostatic microenvironment within shells near the protein surface. Our iterative feature selection process identified features important in other models, as well as features unique to the DBSI model, such as a banded electrostatic feature with spatial separation comparable with the canonical width of the DNA minor groove. Validations and comparisons with established methods using a range of performance metrics clearly demonstrate the predictive advantage of DBSI, and its comparable performance on unbound (APO-29) and bound (HOLO-30) conformations demonstrates robustness to binding-induced protein conformational changes. Finally, we offer our feature data table to others for integration into their own models or for testing improved feature selection and model training strategies based on DBSI.
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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.