ArticleJournal of computational chemistry2008
Insights on protein-DNA recognition by coarse grain modelling.
Article in Journal of computational chemistry, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- BioSpring: An elastic network framework for interactive exploration of macromolecular mechanics.Protein science : a publication of the Protein Society · 2025Article
- Exploring the most stable aptamer/target molecule complex by the stochastic tunnelling-basin hopping-discrete molecular dynamics method.Scientific reports · 2021Article
- The "sugar" coarse-grained DNA model.Journal of molecular modeling · 2017Article
- Integrating multi-scale data on homologous recombination into a new recognition mechanism based on simulations of the RecA-ssDNA/dsDNA structure.Nucleic acids research · 2015Article
- An experimentally-informed coarse-grained 3-Site-Per-Nucleotide model of DNA: structure, thermodynamics, and dynamics of hybridization.The Journal of chemical physics · 2013Article
- Protein-DNA docking with a coarse-grained force field.BMC bioinformatics · 2012Article
- Article
- A coarse-grained model of DNA with explicit solvation by water and ions.The journal of physical chemistry. B · 2011Article
- Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments.Nucleic acids research · 2010Article
- Pushing the limits of what is achievable in protein-DNA docking: benchmarking HADDOCK's performance.Nucleic acids research · 2010Article
- An effective approach for generating a three-Cys2His2 zinc-finger-DNA complex model by docking.BMC bioinformatics · 2010Article
- Coarse-grained model of nucleic acid bases.Journal of computational chemistry · 2010Article
- PRIMO/PRIMONA: a coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy.Proteins · 2010Article
- PTools: an opensource molecular docking library.BMC structural biology · 2009Article
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Authors and funding
4 authors.
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Abstract
Coarse grain modelling of macromolecules is a new approach, potentially well adapted to answer numerous issues, ranging from physics to biology. We propose here an original DNA coarse grain model specifically dedicated to protein-DNA docking, a crucial, but still largely unresolved, question in molecular biology. Using a representative set of protein-DNA complexes, we first show that our model is able to predict the interaction surface between the macromolecular partners taken in their bound form. In a second part, the impact of the DNA sequence and electrostatics, together with the DNA and protein conformations on docking is investigated. Our results strongly suggest that the overall DNA structure mainly contributes in discriminating the interaction site on cognate proteins. Direct electrostatic interactions between phosphate groups and amino acid side chains strengthen the binding. Overall, this work demonstrates that coarse grain modeling can reveal itself a precious auxiliary for a general and complete description and understanding of protein-DNA association mechanisms.
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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.