ArticleJournal of biomolecular NMR2013
Solvated protein-DNA docking using HADDOCK.
Article in Journal of biomolecular NMR, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 27 citations in OpenAlex.
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- Probing Biomolecular Interactions with Paramagnetic Nuclear Magnetic Resonance Spectroscopy.Chembiochem : a European journal of chemical biology · 2025Review
- Searching for Low Probability Opening Events in a DNA Sliding Clamp.Life (Basel, Switzerland) · 2022Article
- The DNA Recognition Motif of GapR Has an Intrinsic DNA Binding Preference towards AT-rich DNA.Molecules (Basel, Switzerland) · 2021Article
- In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1.Informatics in medicine unlocked · 2021Article
- Immunoinformatics and Molecular Docking Studies Predicted Potential Multiepitope-Based Peptide Vaccine and Novel Compounds against Novel SARS-CoV-2 through Virtual Screening.BioMed research international · 2021Article
- Recent Advances in Molecular Docking for the Research and Discovery of Potential Marine Drugs.Marine drugs · 2020Review
- Rational design of an XNA ligase through docking of unbound nucleic acids to toroidal proteins.Nucleic acids research · 2019Article
- In silico modeling of epigenetic-induced changes in photoreceptor cis-regulatory elements.Molecular vision · 2018Article
- Evolution of Macromolecular Docking Techniques: The Case Study of Nickel and Iron Metabolism in Pathogenic Bacteria.Molecules (Basel, Switzerland) · 2015Review
- Structure-based modeling of protein: DNA specificity.Briefings in functional genomics · 2015Review
- NMR studies on protein-nucleic acid interaction.Journal of biomolecular NMR · 2013Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Interfacial water molecules play an important role in many aspects of protein-DNA specificity and recognition. Yet they have been mostly neglected in the computational modeling of these complexes. We present here a solvated docking protocol that allows explicit inclusion of water molecules in the docking of protein-DNA complexes and demonstrate its feasibility on a benchmark of 30 high-resolution protein-DNA complexes containing crystallographically-determined water molecules at their interfaces. Our protocol is capable of reproducing the solvation pattern at the interface and recovers hydrogen-bonded water-mediated contacts in many of the benchmark cases. Solvated docking leads to an overall improvement in the quality of the generated protein-DNA models for cases with limited conformational change of the partners upon complex formation. The applicability of this approach is demonstrated on real cases by docking a representative set of 6 complexes using unbound protein coordinates, model-built DNA and knowledge-based restraints. As HADDOCK supports the inclusion of a variety of NMR restraints, solvated docking is also applicable for NMR-based structure calculations of protein-DNA complexes.
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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.