A detailed description of the dnatco.datmos.org web server implementing the universal structural alphabet of nucleic acids is presented. It is capable of processing any mmCIF- or PDB-formatted files containing DNA or RNA molecules; these can either be uploaded by the user or supplied as the wwPDB or PDB-REDO structural database access code. The web server performs an assignment of the nucleic acid conformations and presents the results for the intuitive annotation, validation, modeling and refinement of nucleic acids.

Laboratory of Biomolecular Recognition Institute of Biotechnology of the Czech Academy of Sciences Prumyslova 595 Vestec Czech Republic

Laboratory of Structural Bioinformatics of Proteins Institute of Biotechnology of the Czech Academy of Sciences Prumyslova 595 Vestec Czech Republic

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Afonine, P. V., Grosse-Kunstleve, R. W., Echols, N., Headd, J. J., Moriarty, N. W., Mustyakimov, M., Terwilliger, T. C., Urzhumtsev, A., Zwart, P. H. & Adams, P. D. (2012). Acta Cryst. D68, 352–367. PubMed PMC

Berman, H. M., Battistuz, T., Bhat, T. N., Bluhm, W. F., Bourne, P. E., Burkhardt, K., Feng, Z., Gilliland, G. L., Iype, L., Jain, S., Fagan, P., Marvin, J., Padilla, D., Ravichandran, V., Schneider, B., Thanki, N., Weissig, H., Westbrook, J. D. & Zardecki, C. (2002). Acta Cryst. D58, 899–907. PubMed

Berman, H. M., Westbrook, J., Feng, Z., Iype, L., Schneider, B. & Zardecki, C. (2002). Acta Cryst. D58, 889–898. PubMed

Biedermannová, L. & Schneider, B. (2016). Biochim. Biophys. Acta, 1860, 1821–1835. PubMed

Burley, S. K., Berman, H. M., Bhikadiya, C., Bi, C., Chen, L., Di Costanzo, L., Christie, C., Dalenberg, K., Duarte, J. M., Dutta, S., Feng, Z., Ghosh, S., Goodsell, D. S., Green, R. K., Guranović, V., Guzenko, D., Hudson, B. P., Kalro, T., Liang, Y., Lowe, R., Namkoong, H., Peisach, E., Periskova, I., Prlić, A., Randle, C., Rose, A., Rose, P., Sala, R., Sekharan, M., Shao, C., Tan, L., Tao, Y.-P., Valasatava, Y., Voigt, M., Westbrook, J., Woo, J., Yang, H., Young, J., Zhuravleva, M. & Zardecki, C. (2019). Nucleic Acids Res. 47, D464–D474. PubMed PMC

Černý, J., Božíková, P. & Schneider, B. (2016). Nucleic Acids Res. 44, W284–W287. PubMed PMC

Černý, J., Božíková, P., Svoboda, J. & Schneider, B. (2020). Nucleic Acids Res. 48, 6367–6381. PubMed PMC

Correll, C. C., Beneken, J., Plantinga, M. J., Lubbers, M. & Chan, Y.-L. (2003). Nucleic Acids Res. 31, 6806–6818. PubMed PMC

Cover, T. & Hart, P. (1967). IEEE Trans. Inf. Theory, 13, 21–27.

Craveur, P., Joseph, A. P., Esque, J., Narwani, T. J., Noël, F., Shinada, N., Goguet, M., Leonard, S., Poulain, P., Bertrand, O., Faure, G., Rebehmed, J., Ghozlane, A., Swapna, L. S., Bhaskara, R. M., Barnoud, J., Téletchéa, S., Jallu, V., Cerny, J., Schneider, B., Etchebest, C., Srinivasan, N., Gelly, J.-C. & de Brevern, A. G. (2015). Front. Mol. Biosci. 2, 20. PubMed PMC

Drew, H. R., Wing, R. M., Takano, T., Broka, C., Tanaka, S., Itakura, K. & Dickerson, R. E. (1981). Proc. Natl Acad. Sci. USA, 78, 2179–2183. PubMed PMC

Duarte, C. M. & Pyle, A. M. (1998). J. Mol. Biol. 284, 1465–1478. PubMed

Feng, Z. (2017). MAXIT version 10.000. https://sw-tools.rcsb.org/apps/MAXIT.

Flores, S. C. & Altman, R. B. (2010). RNA, 16, 1769–1778. PubMed PMC

Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. & Sussman, J. L. (2013). Isr. J. Chem. 53, 207–216.

Heus, H. A. & Pardi, A. (1991). Science, 253, 191–194. PubMed

Humphris-Narayanan, E. & Pyle, A. M. (2012). J. Mol. Biol. 421, 6–26. PubMed PMC

Joosten, R. P., Joosten, K., Murshudov, G. N. & Perrakis, A. (2012). Acta Cryst. D68, 484–496. PubMed PMC

Joosten, R. P., Long, F., Murshudov, G. N. & Perrakis, A. (2014). IUCrJ, 1, 213–220. PubMed PMC

Joseph, A. P., Agarwal, G., Mahajan, S., Gelly, J.-C., Swapna, L. S., Offmann, B., Cadet, F., Bornot, A., Tyagi, M., Valadié, H., Schneider, B., Etchebest, C., Srinivasan, N. & De Brevern, A. G. (2010). Biophys. Rev. 2, 137–147. PubMed PMC

Kabsch, W. & Sander, C. (1983). Biopolymers, 22, 2577–2637. PubMed

Khesbak, H., Savchuk, O., Tsushima, S. & Fahmy, K. (2011). J. Am. Chem. Soc. 133, 5834–5842. PubMed

Kolenko, P., Svoboda, J., Černý, J., Charnavets, T. & Schneider, B. (2020). Submitted. PubMed PMC

Konagurthu, A. S., Lesk, A. M. & Allison, L. (2012). Bioinformatics, 28, i97–i105. PubMed PMC

Leontis, N. B. & Westhof, E. (2001). RNA, 7, 499–512. PubMed PMC

Lu, X.-J., Bussemaker, H. J. & Olson, W. K. (2015). Nucleic Acids Res. 43, e142. PubMed PMC

Nguyen, B., Neidle, S. & Wilson, W. D. (2009). Acc. Chem. Res. 42, 11–21. PubMed PMC

Nicholls, R. A., Long, F. & Murshudov, G. N. (2012). Acta Cryst. D68, 404–417. PubMed PMC

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). J. Mol. Biol. 313, 229–237. PubMed

Peter, E. & Černý, J. (2018). Int. J. Mol. Sci. 19, 3405. PubMed PMC

Peter, E. & Černý, J. (2019). Int. J. Mol. Sci. 20, 370. PubMed PMC

Richardson, J. S., Schneider, B., Murray, L. W., Kapral, G. J., Immormino, R. M., Headd, J. J., Richardson, D. C., Ham, D., Hershkovits, E., Williams, L. D., Keating, K. S., Pyle, A. M., Micallef, D., Westbrook, J. & Berman, H. M. (2008). RNA, 14, 465–481. PubMed PMC

Roh, J. H., Briber, R. M., Damjanovic, A., Thirumalai, D., Woodson, S. A. & Sokolov, A. P. (2009). Biophys. J. 96, 2755–2762. PubMed PMC

Saenger, W. (1984). Principles of Nucleic Acid Structure. New York: Springer.

Schneider, B., Božíková, P., Čech, P., Svozil, D. & Černý, J. (2017). Genes, 8, 278. PubMed PMC

Schneider, B., Božíková, P., Nečasová, I., Čech, P., Svozil, D. & Černý, J. (2018). Acta Cryst. D74, 52–64. PubMed PMC

Schneider, B., Černý, J., Svozil, D., Čech, P., Gelly, J.-C. & de Brevern, A. G. (2014). Nucleic Acids Res. 42, 3381–3394. PubMed PMC

Schneider, B., Morávek, Z. & Berman, H. M. (2004). Nucleic Acids Res. 32, 1666–1677. PubMed PMC

Schneider, B., Patel, K. & Berman, H. M. (1998). Biophys. J. 75, 2422–2434. PubMed PMC

Svozil, D., Kalina, J., Omelka, M. & Schneider, B. (2008). Nucleic Acids Res. 36, 3690–3706. PubMed PMC

Woese, C. R., Winker, S. & Gutell, R. R. (1990). Proc. Natl Acad. Sci. USA, 87, 8467–8471. PubMed PMC

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