ArticleFrontiers in molecular biosciences2022
pyDockDNA: A new web server for energy-based protein-DNA docking and scoring.
Article in Frontiers in molecular biosciences, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed, 41 citations in OpenAlex.
- Performance of pyDock in 8th CAPRI: Energy-Based Scoring Applied to Docking and AlphaFold Models.Proteins · 2026Article
- Dockground: Expanding the Resource to Protein-DNA Complexes.Journal of molecular biology · 2026Article
- DNA Damage Recognition by Bacterial and Human Adenine-DNA Glycosylases: Insights from Non-Canonical Substrates.Biomolecules · 2026Article
- Open-Source Molecular Docking and AI-Augmented Structure-Based Drug Design: Current Workflows, Challenges, and Opportunities.International journal of molecular sciences · 2026Review
- Graph-based deep learning approach for high-throughput protein-DNA interaction scoring.Acta pharmacologica Sinica · 2026Article
- A Review of Current Computational Tools for Peptide-Protein Docking.Journal of computational chemistry · 2026Review
- A Comprehensive In-Silico Pipeline for the Discovery of Non-toxic, Stable Antimicrobial Peptides From Databases for Targeting Multi-Drug ResistantBioinformatics and biology insights · 2026Article
- PTF-Vāc: An explainable and generative deep co-learning encoder-decoder system for ab initio discovery of plant transcription factor binding sites.Plant communications · 2025Article
- The Esc(1-21)-1c Antimicrobial Peptide Inhibits a Specific Transcriptional Activator of the MexAB-OprM Efflux Pump inInternational journal of molecular sciences · 2025Article
- Investigating the Role of OsHDT701 and Other Blast-Associated Negative Regulatory Genes in Indica Rice Cultivar Ranjit Using Combined Wet Lab and Computational Approaches.Molecular biotechnology · 2025Article
- Mechanisms of DNA Damage Recognition by UDG and PARP1 in the Nucleosome.Biomolecules · 2025Article
- Review
- Identification of a novel missense variant in theFrontiers in genetics · 2025Article
- Bioinformatics Approaches for Understanding the Binding Affinity of Protein-Nucleic Acid Complexes.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Cooperative dynamics of PARP-1 zinc-finger domains in the detection of DNA single-strand breaks.Scientific reports · 2024Article
- Structural insight into the Csx1-Crn2 fusion self-limiting ribonuclease of type III CRISPR system.Nucleic acids research · 2024Article
- Gene networks governing the response of a calcareous sponge to future ocean conditions reveal lineage-specificEcology and evolution · 2024Article
- CONSTANS, a HUB for all seasons: How photoperiod pervades plant physiology regulatory circuits.The Plant cell · 2024Review
- Flexible structural arrangement and DNA-binding properties of protein p6 from Bacillus subtillis phage φ29.Nucleic acids research · 2024Article
- MucR fromInternational journal of molecular sciences · 2023Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Proteins and nucleic acids are essential biological macromolecules for cell life. Indeed, interactions between proteins and DNA regulate many biological processes such as protein synthesis, signal transduction, DNA storage, or DNA replication and repair. Despite their importance, less than 4% of total structures deposited in the Protein Data Bank (PDB) correspond to protein-DNA complexes, and very few computational methods are available to model their structure. We present here the pyDockDNA web server, which can successfully model a protein-DNA complex with a reasonable predictive success rate (as benchmarked on a standard dataset of protein-DNA complex structures, where DNA is in B-DNA conformation). The server implements the pyDockDNA program, as a module of pyDock suite, thus including third-party programs, modules, and previously developed tools, as well as new modules and parameters to handle the DNA properly. The user is asked to enter Protein Data Bank files for protein and DNA input structures (or suitable models) and select the chains to be docked. The server calculations are mainly divided into three steps: sampling by FTDOCK, scoring with new energy-based parameters and the possibility of applying external restraints. The user can select different options for these steps. The final output screen shows a 3D representation of the top 10 models and a table sorting the model according to the scoring function selected previously. All these output files can be downloaded, including the top 100 models predicted by pyDockDNA. The server can be freely accessed for academic use (https://model3dbio.csic.es/pydockdna).
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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.