ArticleNucleic acids research2009
3D-DART: a DNA structure modelling server.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 151 papers, 1 of them a synthesis that pooled it.
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Who cites it
151 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Next Generation of Ovarian Cancer Detection Using Aptamers.International journal of molecular sciences · 2023Article
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- Structure and DNA binding analysis of AT-rich interaction domain present in human BAF-B specific subunit BAF250b.Protein science : a publication of the Protein Society · 2022Article
- DNA methylation cues in nucleosome geometry, stability and unwrapping.Nucleic acids research · 2022Article
- Residue interactions affecting the deprotonation of internal guanine moieties in oligodeoxyribonucleotides, calculated by FMO methods.Journal of molecular modeling · 2022Article
- Nearest-Neighbor Effects ModulateBiochemistry · 2022Article
- DNA aptamers masking angiotensin converting enzyme 2 as an innovative way to treat SARS-CoV-2 pandemic.Pharmacological research · 2022Article
- Modelling aptamers with nucleic acid mimics (NAM): From sequence to three-dimensional docking.PloS one · 2022Article
91 more citing papers are in PubMed but not listed here.
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
There is a growing interest in structural studies of DNA by both experimental and computational approaches. Often, 3D-structural models of DNA are required, for instance, to serve as templates for homology modeling, as starting structures for macro-molecular docking or as scaffold for NMR structure calculations. The conformational adaptability of DNA when binding to a protein is often an important factor and at the same time a limitation in such studies. As a response to the demand for 3D-structural models reflecting the intrinsic plasticity of DNA we present the 3D-DART server (3DNA-Driven DNA Analysis and Rebuilding Tool). The server provides an easy interface to a powerful collection of tools for the generation of DNA-structural models in custom conformations. The computational engine beyond the server makes use of the 3DNA software suite together with a collection of home-written python scripts. The server is freely available at http://haddock.chem.uu.nl/dna without any login requirement.
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