A Portal for Three-dimensional Structural Information about Nucleic Acids
As of 15-Mar-2023 number of released structures: 12686
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Nucleic Acid Tools

    DNA

    • DNAproDB, an interactive tool for structural analysis of DNA-protein complexes
      • Sagendorf, J.M., Berman, H.M., Rohs, R. (2017) DNAproDB: an interactive tool for structural analysis of DNA-protein complexes. Nucleic Acids Res 45, W89-W97.
    • Assignment of DNA conformers
      • Svozil, D., Kalina, J., Omelka, M., Schneider, B. (2008) DNA conformations and their sequence preferences. Nucleic Acids Res, 36, 3690–3706.

    RNA

    • RNA Basepair Catalog, a collection of representative base pairs and heatmaps for each base pair family.
    • RNA 3D Motif Atlas, a representative collection of RNA 3D internal and hairpin loop motifs.
      • Petrov, A.I., Zirbel, C.L., Leontis, N.B. (2013) Automated classification of RNA 3D motifs and the RNA 3D motif atlas. RNA.
    • Representative RNA 3D Structure Sets, classification of RNA structures by sequence, structure, and species.
      • Leontis, N.B., & Zirbel, C.L. (2012) In Leontis, N. B., Westhof. E. (ed.), RNA 3D structure analysis and prediction. Springer Berlin Heidelberg Vol. 27, pp. 281-298.
    • RNA Base Triple Atlas, a collection of motifs consisting of two RNA basepairs.
      • Abu Almakarem, A.S., Petrov, A.I., Stombaugh, J., Zirbel, C.L. and Leontis, N.B. (2012) Comprehensive survey and geometric classification of base triples in RNA structures. Nucleic Acids Res, 40, 1407-1423.
    • R3D Align, an application for detailed nucleotide to nucleotide alignments of RNA 3D structures.
      • Rahrig, R.R., Leontis, N.B. and Zirbel, C.L. (2010) R3D Align: global pairwise alignment of RNA 3D structures using local superpositions. Bioinformatics, 26, 2689-2697.
      • Rahrig, R.R., Petrov, A.I., Leontis, N.B. and Zirbel, C.L. (2013) R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures. Nucleic Acids Res, 41, W15-21.
    • WebFR3D, a webserver for symbolic and geometric searching of RNA 3D structures.
      • Sarver, M., Zirbel, C.L., Stombaugh, J., Mokdad, A. and Leontis, N.B. (2008) FR3D: finding local and composite recurrent structural motifs in RNA 3D structures. J Math Biol, 56, 215-252.
    • RNA Viewer, a tool for viewing RNA 2-dimensional structure, base pairs and RNA patterns. 2D structure is fully annotated according to Leontis and Westhof (2001) RNA 7:499-512.
      • Yang, H., Jossinet, F., Leontis, N., Chen, L., Westbrook, J., Berman, H.M. and Westhof, E. (2003) Tools for the automatic identification and classification of RNA base pairs. Nucleic Acids Res, 31, 3450-3460.
    • NASSAM, Nucleic Acid Search for Substructures and Motifs.
      • Firdaus-Raih, M., Harrison, A-M, Willett, P., and Artymiuk, P.J. (2011) Novel base triples in RNA structures revealed by graph theoretical searching methods. BMC Bioinformatics, 12(S13): S2.
      • Harrison, A-M., South, D.R., Willett, P., and Artymiuk, P.J. (2003) Representation, searching and discovery of patterns of bases in complex RNA structures. Journal of Computer-Aided Molecular Design, 17, 537-549.
    • SAVoR, an easy-to-use web application that allows the user to visualize RNA-seq data and other genomic annotations on RNA secondary structures.
      • F. Li, P. Ryvkin, D.M. Childress, O. Valladares, B.D. Gregory, L.S. Wang. (2012) "SAVoR: a server for sequencing annotation and visualization of RNA structures". Nucleic Acids Research.
    • R-chie, a web server and R package for plotting arc diagrams of RNA secondary structures.
      • Lai, D., Proctor, J.R., Zhu, J.Y.A., and Meyer, I.M. (2012) R-chie: a web server and R package for visualizing RNA secondary structures. Nucleic Acids Research.
    • SARA (Structure Alignment of Ribonucleic Acids), is a fully automated method for aligning two RNA structures.
      • Capriotti E, Marti-Renom MA. (2009) SARA: a server for function annotation of RNA structures. Nucleic Acids Res.
    • RNAbow, a program for visualizing RNA base pairing probabilities.
      • Aalberts, D.P. and Jannen, W.K.(2013) Visualizing RNA base pairing probabilities with RNAbow diagrams.RNA 19, 475-478
    • RNA-Puzzles, a CASP-like evaluation of RNA three-dimensional structure prediction.
      • Cruz, J.A., Blanchet, M.F., Boniecki, M., Bujnicki, J.M., Chen, S.J., Cao, S., Das, R., Ding, F., Dokholyan, N.V., Flores, S.C., Huang, L., Lavender, C. A., Lisi, V., Major, F., Mikolajczak, K., Patel, D. J., Philips, A., Puton, T., Santalucia, J., Sijenyi, F., Hermann, T., Rother, K., Rother, M., Serganov, A., Skorupski, M., Soltysinski T., Sripakdeevong, P., Tuszynska, I., Weeks, K. M., Waldsich, C., Wildauer, M., Leontis, N. B., Westhof, E. (2012) RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction. RNA 18, 610-625.
    • SETTER Web Server, a web-server for RNA structure comparison.
      • P. Čech, D. Svozil, D. Hoksza. (2012) SETTER Web Server - the Web Server for RNA Structure Comparison, Nucleid Acids Research, 40(W1), pp.: W42-W48.
    • VARNA, a visualization applet for RNA. Interactive drawing and editing of the RNA secondary structure
      • Kévin Darty, Alain Denise and Yann Ponty Bioinformatics, pp. 1974-1975, Vol. 25, no. 15, 2009
    • Forna, a webserver for displaying 2D diagrams of RNA molecules.
        Kerpedjiev P, Hammer S, Hofacker IL (2015). Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams. Bioinformatics 31(20):3377-9. DOI: 10.1093/bioinformatics/btv372

    DNA & RNA

    • DSSR, an integrated software tool for Dissecting the Spatial Structure of RNA
      • Xiang-Jun Lu, Harmen J. Bussemaker, Wilma K. Olson Nucleic Acids Res (2015) 43 (21): e142. DOI: 10.1093/nar/gkv716
    • RNAfold web server, a tool which predicts secondary structures of single stranded RNA or DNA sequences.
      • Gruber AR, Lorenz R, Bernhart SH, Neuböck R, Hofacker IL.The Vienna RNA Websuite. Nucleic Acids Res. 2008.
      • Lorenz, R. and Bernhart, S.H. and Höner zu Siederdissen, C. and Tafer, H. and Flamm, C. and Stadler, P.F. and Hofacker, I.L. (2011) "ViennaRNA Package 2.0", Algorithms for Molecular Biology, 6, 26.
    • Alignment of RNA Tertiary Structures, a fully automated method for aligning a pair of nucleic acid 3D structures (RNAs or DNAs) and detecting a-priori unknown common substructures.
      • O. Dror, R. Nussinov and H. J. Wolfson (2005). ARTS: alignment of RNA tertiary structures. Proceedings of the 4th European Conference on Computational Biology/6th Meeting of the Spanish Bioinformatics Network (ECCB/JBI'05). Bioinformatics, 21, ii47-ii53.
      • O. Dror, R. Nussinov, and H. J. Wolfson (2006). The ARTS web server for aligning RNA tertiary structures, Nucleic Acids Research, 34, W412-W415.

    Ribosome

    • RiboVision, a modern open-source ribosome-information viewer website.
      • Petrov, A.S., Bernier, C.R. et al. (2013) Secondary structure and domain architecture of the 23S and 5S rRNAs Nucl. Acids Res.

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