ArticleBioinformatics (Oxford, England)2010
Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function.
Article in Bioinformatics (Oxford, England), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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41 citing papers in PubMed.
- DeepPANB: integrating protein language model with PaiNN equivariant graph neural networks for prediction of protein-nucleic acid binding sites.Briefings in bioinformatics · 2026Article
- CAP: Commutative algebra prediction of protein-nucleic acid binding affinities.Machine learning: science and technology · 2025Article
- DRBP-EDP: classification of DNA-binding proteins and RNA-binding proteins using ESM-2 and dual-path neural network.NAR genomics and bioinformatics · 2025Article
- ProkDBP: Toward more precise identification of prokaryotic DNA binding proteins.Protein science : a publication of the Protein Society · 2024Article
- 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
- Ab initio predictions for 3D structure and stability of single- and double-stranded DNAs in ion solutions.PLoS computational biology · 2022Article
- Research on DNA-Binding Protein Identification Method Based on LSTM-CNN Feature Fusion.Computational and mathematical methods in medicine · 2022Article
- DNAPred_Prot: Identification of DNA-Binding Proteins Using Composition- and Position-Based Features.Applied bionics and biomechanics · 2022Article
- PreDBA: A heterogeneous ensemble approach for predicting protein-DNA binding affinity.Scientific reports · 2020Article
- DLIGAND2: an improved knowledge-based energy function for protein-ligand interactions using the distance-scaled, finite, ideal-gas reference state.Journal of cheminformatics · 2019Article
- An SVM-based method for assessment of transcription factor-DNA complex models.BMC bioinformatics · 2018Article
- iDNAProt-ES: Identification of DNA-binding Proteins Using Evolutionary and Structural Features.Scientific reports · 2017Article
- Identification of DNA-Binding Proteins Using Mixed Feature Representation Methods.Molecules (Basel, Switzerland) · 2017Article
- PSFM-DBT: Identifying DNA-Binding Proteins by Combing Position Specific Frequency Matrix and Distance-Bigram Transformation.International journal of molecular sciences · 2017Article
- Improved detection of DNA-binding proteins via compression technology on PSSM information.PloS one · 2017Article
- Resurrecting ancestral structural dynamics of an antiviral immune receptor: adaptive binding pocket reorganization repeatedly shifts RNA preference.BMC evolutionary biology · 2016Article
- Identification of DNA-binding proteins using multi-features fusion and binary firefly optimization algorithm.BMC bioinformatics · 2016Article
- BindUP: a web server for non-homology-based prediction of DNA and RNA binding proteins.Nucleic acids research · 2016Article
- DNABP: Identification of DNA-Binding Proteins Based on Feature Selection Using a Random Forest and Predicting Binding Residues.PloS one · 2016Article
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3 authors.
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Abstract
motivationTemplate-based prediction of DNA binding proteins requires not only structural similarity between target and template structures but also prediction of binding affinity between the target and DNA to ensure binding. Here, we propose to predict protein-DNA binding affinity by introducing a new volume-fraction correction to a statistical energy function based on a distance-scaled, finite, ideal-gas reference (DFIRE) state.
resultsWe showed that this energy function together with the structural alignment program TM-align achieves the Matthews correlation coefficient (MCC) of 0.76 with an accuracy of 98%, a precision of 93% and a sensitivity of 64%, for predicting DNA binding proteins in a benchmark of 179 DNA binding proteins and 3797 non-binding proteins. The MCC value is substantially higher than the best MCC value of 0.69 given by previous methods. Application of this method to 2235 structural genomics targets uncovered 37 as DNA binding proteins, 27 (73%) of which are putatively DNA binding and only 1 protein whose annotated functions do not contain DNA binding, while the remaining proteins have unknown function. The method provides a highly accurate and sensitive technique for structure-based prediction of DNA binding proteins. AVAILABILITY: The method is implemented as a part of the Structure-based function-Prediction On-line Tools (SPOT) package available at http://sparks.informatics.iupui.edu/spot
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