Web DSSR for dissecting the spatial structures of nucleic acids
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wDSSR (web DSSR) is a user-friendly web-based interface to the DSSR software package for the analysis and visualization of three-dimensional nucleic acid-containing structures, including their complexes with proteins and other ligands. Although this versatile and integrated suite of programs is widely used in the scientific community, its command-line-driven style is not especially user-friendly, for either novices (non-Linux/Unix users) or educational purposes.
Our new web-based interface provides straightforward access to some of the most popular features of the software, including:
The analysis component determines a wide range of conformational parameters — such as the identities and rigid-body parameters of interacting nucleic-acid bases and base-pair steps, the nucleotides comprising helical fragments, etc. — from a user-uploaded PDB-formatted file or a PDB ID. The output files can be viewed on the web or downloaded. Selected sequence and base-pairing information is reported in Grid-view tables with sorting and searching capabilities.
The visualization component creates secondary structure, allowing for simultaneously highlighting 1D, 2D, and 3D nucleic-acid structures. The server takes a user-uploaded PDB file or a PDB ID, and returns 1D, 2D, and 3D representations of the structure.
The server contains a database of pre-analyzed nucleic-acid-containing PDB structures to facilitate user access.
2. Lu X-J. & Olson W.K. (2008) 3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three dimensional nucleic-acid structures, Nature Protocols, 3(7) 1213-1227
Users interested in learning more about the content and capabilities of 3DNA should consult (i) the above references, (ii) the tutorial and worked-out examples found at the 3DNA website, and (iii) the user interchange at the 3DNA forum.
The following article describes the standard base reference frames, developed by the structural biology community and used in the 3DNA determination of rigid-body conformational parameters.
Olson, W.K., Bansal, M., Burley, S.K., Dickerson, R.E., Gerstein, M., Harvey, S.C., Heinemann, U., Lu, X.-J., Neidle, S., Shakked, Z., Sklenar, H., Suzuki, M., Tung, C.S., Westhof, E., Wolberger, C. & Berman, H.M. (2001) A standard reference frame for the description of nucleic acid base-pair geometry. J. Mol. Biol. 313(1), 229-237
The conformational parameters for different types of nucleic-acid structures, reported in the following papers, provide useful benchmarks against which other structures can be compared.
Olson, W.K., Colasanti, A.V., Li, Y , Ge, W. , Zheng, G. & Zhurkin, V.B. (2006) DNA simulation benchmarks as revealed by X-ray structures. In Computational Studies of RNA and DNA, J. Sponer & F. Lankas , Eds., Springer, Dordrecht, The Netherlands, pp. 235-257.
Olson, W.K., Colasanti, A.V., Lu, X.-J. & Zhurkin, V.B. (2008) Physico-chemical properties of nucleic acids: character and recognition of Watson-Crick base pairs. In Wiley Encyclopedia of Chemical Biology, John Wiley & Sons, New York, doi: 10.1002/9780470048672.wecb452.
Olson, W.K., Colasanti, A.V., Czapla, L. & Zheng, G. (2009) Insights into the sequence-dependent macromolecular properties of DNA from base-pair level modeling. In Coarse-Graining of Condensed Phase and Biomolecular Systems, G.A. Voth, Ed., CRC Press, Taylor & Francis Group, Boca Raton, FL, pp. 205-223.
Olson, W.K., Srinivasan, A.R., Colasanti, A.V., Zheng, G. & Swigon. D. (2009) DNA biomechanics. In Handbook of Molecular Biophysics: Methods and Applications, H.G. Bohr, Ed., WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim, in press.
The following papers pinpoint the differences among the programs most frequently used in the analysis of nucleic-acid structures: