ArticleNucleic acids research1998
Quantitative parameters for amino acid-base interaction: implications for prediction of protein-DNA binding sites.
Article in Nucleic acids research, 1998. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed.
- RGTBind: RBF-gate graph transformer with spatially biased attention for protein-DNA binding-site prediction.Journal of molecular modeling · 2026Article
- EGPDI: identifying protein-DNA binding sites based on multi-view graph embedding fusion.Briefings in bioinformatics · 2024Article
- How acidic amino acid residues facilitate DNA target site selection.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Insights into DNA solvation found in protein-DNA structures.Biophysical journal · 2022Review
- ProDFace: A web-tool for the dissection of protein-DNA interfaces.Frontiers in molecular biosciences · 2022Article
- On the prediction of DNA-binding preferences of C2H2-ZF domains using structural models: application on human CTCF.NAR genomics and bioinformatics · 2020Article
- PreDBA: A heterogeneous ensemble approach for predicting protein-DNA binding affinity.Scientific reports · 2020Article
- DNA Motif Recognition Modeling from Protein Sequences.iScience · 2018Article
- EL_PSSM-RT: DNA-binding residue prediction by integrating ensemble learning with PSSM Relation Transformation.BMC bioinformatics · 2017Article
- An efficient algorithm for improving structure-based prediction of transcription factor binding sites.BMC bioinformatics · 2017Article
- Direct Comparison of Amino Acid and Salt Interactions with Double-Stranded and Single-Stranded DNA from Explicit-Solvent Molecular Dynamics Simulations.Journal of chemical theory and computation · 2017Article
- Structure-based prediction of transcription factor binding specificity using an integrative energy function.Bioinformatics (Oxford, England) · 2016Article
- PDNAsite: Identification of DNA-binding Site from Protein Sequence by Incorporating Spatial and Sequence Context.Scientific reports · 2016Article
- Sequence-Specific Recognition of DNA by Proteins: Binding Motifs Discovered Using a Novel Statistical/Computational Analysis.PloS one · 2016Article
- An overview of the prediction of protein DNA-binding sites.International journal of molecular sciences · 2015Review
- A systematic survey of the Cys2His2 zinc finger DNA-binding landscape.Nucleic acids research · 2015Article
- Mesoscopic model and free energy landscape for protein-DNA binding sites: analysis of cyanobacterial promoters.PLoS computational biology · 2014Article
- Absence of a simple code: how transcription factors read the genome.Trends in biochemical sciences · 2014Review
- Diversification of transcription factor paralogs via noncanonical modularity in C2H2 zinc finger DNA binding.Molecular cell · 2014Article
- Bioinformatic analysis of the protein/DNA interface.Nucleic acids research · 2014Article
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2 authors.
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Abstract
Inspection of the amino acid-base interactions in protein-DNA complexes is essential to the understanding of specific recognition of DNA target sites by regulatory proteins. The accumulation of information on protein-DNA co-crystals challenges the derivation of quantitative parameters for amino acid-base interaction based on these data. Here we use the coordinates of 53 solved protein-DNA complexes to extract all non-homologous pairs of amino acid-base that are in close contact, including hydrogen bonds and hydrophobic interactions. By comparing the frequency distribution of the different pairs to a theoretical distribution and calculating the log odds, a quantitative measure that expresses the likelihood of interaction for each pair of amino acid-base could be extracted. A score that reflects the compatibility between a protein and its DNA target can be calculated by summing up the individual measures of the pairs of amino acid-base involved in the complex, assuming additivity in their contributions to binding. This score enables ranking of different DNA binding sites given a protein binding site and vice versa and can be used in molecular design protocols. We demonstrate its validity by comparing the predictions using this score with experimental binding results of sequence variants of zif268 zinc fingers and their DNA binding sites.
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