The DOI matches its Crossref record; 13 of the 13 references it cites were found in a registry or an index.
3D-DART: a DNA structure modelling server
Open accessAbstract
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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Numerical data and functional relationships in science and technology
Bechmann, R., Hearmon, R. F. S., & Kurtz, S. K. (1969) · Springer eBooks · Cited by 5,858
HADDOCK: A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information
Dominguez, C., Boelens, R., & Bonvin, A. M. J. J. (2003) · Journal of the American Chemical Society · doi:10.1021/ja026939x · Cited by 3,187
Self-citationLu, X.-J. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg680 · Cited by 1,660
Landolt-Börnstein, Numerical Data and Functional Relationships in Science and Technology
Green, L. C. (1967) · American Journal of Physics · doi:10.1119/1.1974060 · Cited by 704
HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets
de Vries, S. J., van Dijk, A. D. J., Krzeminski, M., van Dijk, M., Thureau, A., Hsu, V., Wassenaar, T., & Bonvin, A. M. J. J. (2007) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.21723 · Cited by 556
Self-citationProtein-DNA interactions: a structural analysis
Jones, S., van Heyningen, P., Berman, H. M., & Thornton, J. M. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.2659 · Cited by 424
DNA bending: the prevalence of kinkiness and the virtues of normality
Dickerson, R. (1998) · Nucleic Acids Research · doi:10.1093/nar/26.8.1906 · Cited by 383
Molecular Modeling of Nucleic Acids
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DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI
Flick, K. E., Jurica, M. S., Monnat, R. J., & Stoddard, B. L. (1998) · Nature · doi:10.1038/27952 · Cited by 246
Information-driven protein-DNA docking using HADDOCK: it is a matter of flexibility
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Cited by
DNA punch cards for storing data on native DNA sequences via enzymatic nicking
Tabatabaei, S. K., Wang, B., Athreya, N. B. M., Enghiad, B., Hernandez, A. G., Fields, C. J., Leburton, J.-P., Soloveichik, D., Zhao, H., & Milenkovic, O. (2020) · Nature Communications · doi:10.1038/s41467-020-15588-z · Cited by 120
Kurkcuoglu, Z., & Bonvin, A. M. J. J. (2020) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25802 · Cited by 37
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Metadata
- Authors
- van Dijk, M., & Bonvin, A. M. J. J.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-05-05
- Volume
- 37
- Issue
- Web Server
- Pages
- W235-W239
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2132213868
- Cited by
- 340
- References
- 13
- FWCI
- 2.64
- Type
- journal article
- Language
- en
- Open access
- gold
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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