References
- [1] Adamiak R.W., Blazewicz J., Formanowicz P., Gdaniec Z., Kasprzak M., Popenda M., Szachniuk M., An algorithm for an automatic NOE pathways analysis of 2D NMR spectra of RNA duplexes, Journal of Computational Biology,11, 2004, 163-180.
- [2] Antczak M., Blazewicz J., Lukasiak P., Milostan M., Krasnogor N., Palik G., DomAns-Pattern based method for protein domain boundaries prediction and analysis, Foundations of Computing and Decision Sciences, 36, 2011, 99-119.
- [3] Antczak M., Zok T., Popenda M., Lukasiak P., Adamiak R.W., Blazewicz J., Szachniuk M., RNApdbee - a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs, Nucleic Acids Research, 42, 2014, W368-W372.
- [4] Antczak M., Popenda M., Zok T., Sarzynska J., Ratajczak T., Tomczyk K., Adamiak R.W., Szachniuk M., New functionality of RNAComposer: an application to shape the axis of miR160 precursor structure, Acta Biochimica Polonica, 63, 2016, 737-744.
- [5] Antczak M., Popenda M., Zok T., Zurkowski M., Adamiak R.W., Szachniuk M., New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation, Bioinformatics, 34, 2018, 1304-1312.
- [6] Antczak M., Zok T., Osowiecki M., Popenda M., Adamiak R.W., Szachniuk M., RNAfitme: a webserver for modeling nucleobase and nucleoside residue conformation in fixed-backbone RNA structures, BMC Bioinformatics, 19, 2018, 304.
- [7] Antczak M., Zablocki M., Zok T., Rybarczyk A., Blazewicz J., Szachniuk M., RNAvista: a webserver to assess RNA secondary structures with non-canonical base pairs, Bioinformatics, 35, 2019, 152-155.
- [8] Backofen R., Engelhardt J., Erxleben A., Fallmann J., Grüning B., Ohlerd U., Rajewsky N., Stadler P.F., RNA-bioinformatics: Tools, services and databases for the analysis of RNA-based regulation, Journal of Biotechnology, 261, 2017, 76-84.
- [9] Benson D., Karsch-Mizrachi I., Lipman D., Ostell J., Wheeler D., Genbank, Nucleic Acids Research, 35, 2007, D21-D25.
- [10] Berman H.M., The protein data bank: a historical perspective, Acta Crystallographica Section A, 64, 2007, 88-95.
- [11] Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E., The Protein Data Bank, Nucleic Acids Research, 28, 2000, 235-242.
- [12] Bhagat J., Tanoh F., Nzuobontane E., Laurent T., Orlowski J., Roos M., Wolstencroft K., Aleksejevs S., Stevens R., Pettifer S., Lopez R., Goble C.A., BioCatalogue: a universal catalogue of web services for the life sciences, Nucleic Acids Research, 38, 2010, 689-694.
- [13] Blazewicz J., Figlerowicz M., Kasprzak M., Nowacka M., Rybarczyk A., RNA Partial Degradation Problem: Motivation, Complexity, Algorithm, Journal of Computational Biology, 18, 2011, 821-834.
- [14] Brion P., Westhof E., Hierarchy and dynamics of RNA folding, Annual Review of Biophysics and Biomolecular Structure, 26, 1997, 113-137.
- [15] Chen V.B., Arendall W.B. 3rd, Headd J.J., Keedy D.A., Immormino R.M., Kapral G.J., Murray L.W., Richardson J.S., Richardson D.C., MolProbity: all-atom structure validation for macromolecular crystallography, Acta Crystallographica. Section D, Biological crystallography, 66, 2010, 12-21.
- [16] Chen L., Heikkinen L., Wang C.L., Yang Y., Knott K.E., Wong G., miRToolsGallery: A microRNA bioinformatics resources database portal, Database (Oxford), 2018, bay004.
- [17] 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., RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction, RNA, 18, 2012, 610-625.
- [18] Danaee P., Rouches M., Wiley M., Deng D., Huang L., Hendrix D., bpRNA: largescale automated annotation and analysis of RNA secondary structure, Nucleic Acids Research, 46, 2018, 5381-5394.
- [19] Dawson W.K., Bujnicki J.M., Computational modeling of RNA 3D structures and interactions, Current Opinion in Structural Biology, 37, 2016, 22-28.
- [20] Deigan K.E., Li T.W., Mathews D.H., Weeks K.M., Accurate SHAPE-directed RNA structure determination, Proceedings of National Academy of Sciences USA, 106, 2009, 97-102.
- [21] Gudanis D., Popenda L., Szpotkowski K., Kierzek R., Gdaniec Z., Structural characterization of a dimer of RNA duplexes composed of 8-bromoguanosine modified CGG trinucleotide repeats: a novel architecture of RNA quadruplexes, Nucleic Acids Research,44, 2016, 2409-2416.
- [22] Hall S.R., Allen F.H., Brown I.D., The Crystallographic Information File (CIF): a new standard archive file for crystallography, Acta Crystallographica, A47, 1991, 655-685.
- [23] Honer zu Siederdissen C., Bernhart S.H., Stadler P.F., Hofacker I.L., A folding algorithm for extended RNA secondary structures, Bioinformatics, 27, 2011, i129-i136.
- [24] IUPAC-IUB Commission on Biochemical Nomenclature, Abbreviations and symbols for nucleic acids, polynucleotides, and their constituents, Biochemistry, 9, 1970, 4022-4027.
- [25] Johnson A.D., An extended IUPAC nomenclature code for polymorphic nucleic acids, Bioinformatics, 26, 2010, 1386-1389.
- [26] Kabsch W., A solution for the best rotation to relate two sets of vectors, Acta Crystallographica, A32, 1976, 922-923.
- [27] Kulikova T., Akhtar R., Aldebert P., Althorpe N., Andersson M., Baldwin A., Bates K., Bhattacharyya S., Bower L., Browne P., Castro M., Cochrane G., Duggan K., Eberhardt R., Faruque N., Hoad G., Kanz C., Lee C., Leinonen R., Lin Q., Lombard V., Lopez R., Lorenc D., McWilliam H., Mukherjee G., Nardone F., Pastor M.P., Plaister S., Sobhany S., Stoehr P., Vaughan R., Wu D., Zhu W., Apweiler R., EMBL nucleotide sequence database in 2006, Nucleic Acids Research, 35, 2007, D16-D20.
- [28] Leontis N.B., Westhof E., Geometric nomenclature and classification of RNA base pairs, RNA, 7, 2001, 499-512.
- [29] Lorenz R., Bernhart S.H., Höner zu Siederdissen C., Tafer H., Flamm C., Stadler P.F., Hofacker I.L., ViennaRNA Package 2.0, Algorithms for Molecular Biology, 6, 2011, 26.
- [30] Lukasiak P., Antczak M., Ratajczak T., Bujnicki J.M., Szachniuk M., Popenda M., Adamiak R.W., Blazewicz J., RNAlyzer – novel approach for quality analysis of RNA structural models, Nucleic Acids Research,41, 2013, 5978-90.
- [31] Lukasiak P., Antczak M., Ratajczak T., Szachniuk M., Popenda M., Adamiak R.W., Blazewicz J., RNAssess - a webserver for quality assessment of RNA 3D structures, Nucleic Acids Research,43, 2015, W502-W506.
- [32] Mathews D.H., Disney M.D., Childs J.L., Schroeder S.J., Zuker M., Turner D.H., Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure, Proceedings of National Academy of Sciences USA, 101, 2004, 7287-7292.
- [33] Mathews D.H., Turner D.H., Prediction of RNA secondary structure by free energy minimization, Current Opinion in Structural Biology, 16, 2006, 270-278.
- [34] Miao Z., Westhof E., RNA Structure: Advances and Assessment of 3D Structure Prediction, Annual Review of Biophysics, 46, 2017, 483-503.
- [35] Miskiewicz J., Szachniuk M., Discovering structural motifs in miRNA precursors from Viridiplantae kingdom, Molecules, 23, 6, 2018, 1367.
- [36] Moult J., Fidelis K., Kryshtafovych A., Schwede T., Tramontano A., Critical assessment of methods of protein structure prediction (CASP)-Round XII, Proteins, 86, 2018, 7-15.
- [37] Narayanan B.C., Westbrook J., Ghosh S., Petrov A.I., Sweeney B., Zirbel C.L., Leontis N.B., Berman H.M., The Nucleic Acid Database: new features and capabilities, Nucleic Acids Research, 42, 2014, D114–D122.
- [38] Pang P.S., Elazar M., Pham E.A., Glenn J.S., Simplified RNA secondary structure mapping by automation of SHAPE data analysis, Nucleic Acids Research, 39, 2011, e151.
- [39] Parisien M., Cruz J.A., Westhof E., Major F., New metrics for comparing and assessing discrepancies between RNA 3D structures and models, RNA, 15, 2009, 1875-1885.
- [40] Pearson W.R., Lipman D.J., Improved tools for biological sequence comparison, Proceedings of the National Academy of Sciences of the United States of America, 85, 1988, 2444-2448.
- [41] Popenda L., Bielecki L., Gdaniec Z., Adamiak R.W., Structure and dynamics of adenosine bulged RNA duplex reveals formation of the dinucleotide platform in the C:G-A triple, Arkivoc: Archive for Organic Chemistry, 3, 2009, 130-144.
- [42] Popenda M., Blazewicz M., Szachniuk M., Adamiak R.W., RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures, Nucleic Acids Research, 36, 2008, D386-D391.
- [43] Popenda M., Szachniuk M., Blazewicz M., Wasik S., Burke E.K., Blazewicz J., Adamiak R.W., RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures, BMC Bioinformatics, 11, 2010, 231.
- [44] Popenda M., Szachniuk M., Antczak M., Purzycka K.J., Lukasiak P., Bartol N., Blazewicz J., Adamiak R.W., Automated 3D structure composition for large RNAs, Nucleic Acids Research, 40, 2012, e112.
- [45] Prlic A., Yates A., Bliven S.E., Rose P.W., Jacobsen J., Troshin P.V., Chapman M., Gao J., Koh C.H., Foisy S., Holland R., Rimsa G., Heuer M.L., Brandstätter–Müller H., Bourne P.E., Willis S., BioJava: an open-source framework for bioinformatics in 2012, Bioinformatics, 28, 2012 2693–2695.
- [46] Purzycka K.J., Popenda M., Szachniuk M., Antczak M., Lukasiak P., Blazewicz J., Adamiak R.W., Automated 3D RNA structure prediction using the RNAComposer method for riboswitches, in: S.-J. Chen, D.H. Burke-Aguero (eds.), Methods in Enzymology: Computational Methods for Understanding Riboswitches, 553, Elsevier, 2014, 3-34.
- [47] Puton T., Kozlowski L.P., Rother K.M., Bujnicki J.M., CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction, Nucleic Acids Research, 41, 2013, 4307-4323.
- [48] Rybarczyk A., Szostak N., Antczak M., Zok T., Popenda M., Adamiak R.W., Blazewicz J., Szachniuk M., New in silico approach to assessing RNA secondary structures with non-canonical base pairs, BMC Bioinformatics, 16, 2015, 276.
- [49] Seetin M.G., Mathews D.H., RNA structure prediction: an overview of methods, Methods of Molecular Biology, 905, 2012, 99-122.
- [50] Stevens R.D., Robinson A.J., Goble C.A., MyGrid: Personalised bioinformatics on the information grid, Bioinformatics, 19, 2003, i302-i304.
- [51] Sugawara H., Ogasawara O., Okubo K., Gojobori T., Tateno Y., Ddbj with new system and face, Nucleic Acids Research, 36, 2008, D22-D24.
- [52] Szachniuk M., Assigning NMR Spectra of Irregular RNAs by Heuristic Algorithms, Bulletin of the Polish Academy of Sciences Technical Sciences,63, 2015, 329-338.
- [53] Turner D.H., Mathews D.H., RNA Structure Determination: Methods and Protocols, Springer, New York, 2016.
- [54] Wiedemann J., Zok T., Milostan M., Szachniuk M., LCS-TA to identify similar fragments in RNA 3D structures, BMC Bioinformatics, 18, 2017, 456.
- [55] Wojciechowski P., Frohmberg W., Kierzynka M., Zurkowski P., Blazewicz J., GMAPSEQ– a new method for mapping reads to a reference genome, Foundations of Computing and Decision Sciences, 41, 2016, 123-142.
- [56] wwPDB consortium, Protein Data Bank: the single global archive for 3D macromolecular structure data, Nucleic Acids Research, 47, 2019, D520–D528.
- [57] Zok T., Popenda M., Szachniuk M., MCQ4Structures to compute similarity of molecule structures, Central European Journal of Operations Research, 22, 2014, 457-474.
- [58] Zok T., Antczak M., Riedel M., Nebel D., Villmann T., Lukasiak P., Blazewicz J., Szachniuk M., Building the library of RNA 3D nucleotide conformations using clustering approach, International Journal of Applied Mathematics and Computer Science,25, 2015, 689-700.
- [59] Zok T., Antczak M., Zurkowski M., Popenda M., Blazewicz J., Adamiak R.W., Szachniuk M., RNApdbee 2.0: multifunctional tool for RNA structure annotation, Nucleic Acids Research, 46, 2018, W30-W35.