ArticleNucleic acids research2018
FoldX accurate structural protein-DNA binding prediction using PADA1 (Protein Assisted DNA Assembly 1).
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 37 citations in OpenAlex.
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- Artificial intelligence and first-principle methods in protein redesign: A marriage of convenience?Protein science : a publication of the Protein Society · 2025Article
- A computational workflow for analysis of missense mutations in precision oncology.Journal of cheminformatics · 2024Article
- PredictONCO: a web tool supporting decision-making in precision oncology by extending the bioinformatics predictions with advanced computing and machine learning.Briefings in bioinformatics · 2023Article
- Computational design of novel Cas9 PAM-interacting domains using evolution-based modelling and structural quality assessment.PLoS computational biology · 2023Article
- Correspondence between functional scores from deep mutational scans and predicted effects on protein stability.Protein science : a publication of the Protein Society · 2023Article
- Bacterial expression of a designed single-chain IL-10 prevents severe lung inflammation.Molecular systems biology · 2023Article
- Identification of Heme Oxygenase-1 as a Putative DNA-Binding Protein.Antioxidants (Basel, Switzerland) · 2022Article
- LYRUS: a machine learning model for predicting the pathogenicity of missense variants.Bioinformatics advances · 2022Article
- HISNAPI: a bioinformatic tool for dynamic hot spot analysis in nucleic acid-protein interface with a case study.Briefings in bioinformatics · 2021Article
- Methods for Molecular Modelling of Protein Complexes.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Gene Editing in Pluripotent Stem Cells and Their Derived Organoids.Stem cells international · 2021Review
- Computational structure modeling for diverse categories of macromolecular interactions.Current opinion in structural biology · 2020Review
- ProteinFishing: a protein complex generator within the ModelX toolsuite.Bioinformatics (Oxford, England) · 2020Article
- Protein-assisted RNA fragment docking (RnaX) for modeling RNA-protein interactions using ModelX.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Rational design of an XNA ligase through docking of unbound nucleic acids to toroidal proteins.Nucleic acids research · 2019Article
- Structural Perspective on Revealing and Altering Molecular Functions of Genetic Variants Linked with Diseases.International journal of molecular sciences · 2019Review
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The speed at which new genomes are being sequenced highlights the need for genome-wide methods capable of predicting protein-DNA interactions. Here, we present PADA1, a generic algorithm that accurately models structural complexes and predicts the DNA-binding regions of resolved protein structures. PADA1 relies on a library of protein and double-stranded DNA fragment pairs obtained from a training set of 2103 DNA-protein complexes. It includes a fast statistical force field computed from atom-atom distances, to evaluate and filter the 3D docking models. Using published benchmark validation sets and 212 DNA-protein structures published after 2016 we predicted the DNA-binding regions with an RMSD of <1.8 Å per residue in >95% of the cases. We show that the quality of the docked templates is compatible with FoldX protein design tool suite to identify the crystallized DNA molecule sequence as the most energetically favorable in 80% of the cases. We highlighted the biological potential of PADA1 by reconstituting DNA and protein conformational changes upon protein mutagenesis of a meganuclease and its variants, and by predicting DNA-binding regions and nucleotide sequences in proteins crystallized without DNA. These results opens up new perspectives for the engineering of DNA-protein interfaces.
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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.