Web 3DNA for analysis, reconstruction and visualization of nucleic-acid structures


About


w3DNA (web 3DNA) is a user-friendly web-based interface to the 3DNA software package (1,2) for the analysis, reconstruction, 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:

Analysis:

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/NDB 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.

Reconstruction:

The reconstruction component allows the user to build three-dimensional models of arbitrary sequence and helical types, including 55 different fiber models and customized double-helical structures with base pairs and base-pair steps arranged according to user-supplied rigid-body parameters. The output includes a PDB-formatted file of the nucleic-acid base-pair atoms or an all-atom file with approximate sugar-phosphate backbones, and links for visualization via Webmol (3) or Jmol (4). The user can also construct models of DNA ‘decorated’ with proteins and other molecules by providing the requisite DNA-ligand structural templates and the locations of the binding sites.

Visualization:

The visualization component creates vector-based drawings and scenes that can be rendered as raster-graphics images, allowing for easy generation of publication-quality figures. The server takes a user-uploaded PDB file or a PDB/NDB ID, and returns various representations of the structure, such as Calladine-Drew base and base-pair ‘block’ images in Alchemy format, nucleic acid segments with superimposed ribbon diagrams of bound proteins in raster3D format, etc.

The server contains a database of pre-analyzed nucleic-acid-containing PDB/NDB structures to facilitate user access. Ensembles of NMR or simulated structures can be treated.

References:

1. Lu X-J. & Olson W.K. (2003) 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures, Nucleic Acids Res. 31(17), 5108-5121

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

3. Walther, D. (1997), WebMol: a Java-based PDB viewer. Trends Biochem. Sci., 22, 274-275.

4. Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org.

Additional Readings:

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.

Xin, Y. & Olson, W.K. (2009) BPS: a database of RNA base-pair structures. Nucleic Acids Res. 37(Database issue), D83-D88.

Olson, W.K., Esguerra, M., Xin, Y. & Lu, X.-J. (2009) New information content in RNA base pairing deduced from quantitative analysis of high-resolution structures. Methods 47(3), 177-86.

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.

Balasubramanian S., Xu F. & Olson W.K. (2009) DNA sequence-directed organization of chromatin: structure-based computational analysis of nucleosome-binding sequences, Biophys. J. 96(6), 2245-2260.

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:

Lu, X.-J. & Olson, W.K. (1999) Resolving the discrepancies among nucleic acid conformational analyses. J. Mol. Biol. 285(4), 1563-1575.

Lu, X.-J., Babcock, M.S. & Olson, W.K. (1999) Overview of nucleic acid analysis programs. J. Biomol. Struct. Dynam. 16(4), 833-843.

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