RNApolis: Computational Platform for RNA Structure Analysis

Open access


In the 1970s, computer scientists began to engage in research in the field of structural biology. The first structural databases, as well as models and methods supporting the analysis of biomolecule structures, started to be created. RNA was put at the centre of scientific interest quite late. However, more and more methods dedicated to this molecule are currently being developed. This paper presents RNApolis - a new computing platform, which offers access to seven bioinformatic tools developed to support the RNA structure study. The set of tools include a structural database and systems for predicting, modelling, annotating and evaluating the RNA structure. RNApolis supports research at different structural levels and allows the discovery, establishment, and validation of relationships between the primary, secondary and tertiary structure of RNAs. The platform is freely available at http://rnapolis.pl

If the inline PDF is not rendering correctly, you can download the PDF file here.

  • [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 Sciences36 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 Research42 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 Polonica63 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 Bioinformatics34 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 Bioinformatics19 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 Bioinformatics35 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 Biotechnology261 2017 76-84.

  • [9] Benson D. Karsch-Mizrachi I. Lipman D. Ostell J. Wheeler D. Genbank Nucleic Acids Research35 2007 D21-D25.

  • [10] Berman H.M. The protein data bank: a historical perspective Acta Crystallographica Section A64 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 Research28 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 Research38 2010 689-694.

  • [13] Blazewicz J. Figlerowicz M. Kasprzak M. Nowacka M. Rybarczyk A. RNA Partial Degradation Problem: Motivation Complexity Algorithm Journal of Computational Biology18 2011 821-834.

  • [14] Brion P. Westhof E. Hierarchy and dynamics of RNA folding Annual Review of Biophysics and Biomolecular Structure26 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 DBiological crystallography66 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 RNA18 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 Research46 2018 5381-5394.

  • [19] Dawson W.K. Bujnicki J.M. Computational modeling of RNA 3D structures and interactions Current Opinion in Structural Biology37 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 USA106 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 CrystallographicaA47 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 Bioinformatics27 2011 i129-i136.

  • [24] IUPAC-IUB Commission on Biochemical Nomenclature Abbreviations and symbols for nucleic acids polynucleotides and their constituents Biochemistry9 1970 4022-4027.

  • [25] Johnson A.D. An extended IUPAC nomenclature code for polymorphic nucleic acids Bioinformatics26 2010 1386-1389.

  • [26] Kabsch W. A solution for the best rotation to relate two sets of vectors Acta CrystallographicaA32 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 Research35 2007 D16-D20.

  • [28] Leontis N.B. Westhof E. Geometric nomenclature and classification of RNA base pairs RNA7 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 Biology6 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 USA101 2004 7287-7292.

  • [33] Mathews D.H. Turner D.H. Prediction of RNA secondary structure by free energy minimization Current Opinion in Structural Biology16 2006 270-278.

  • [34] Miao Z. Westhof E. RNA Structure: Advances and Assessment of 3D Structure Prediction Annual Review of Biophysics46 2017 483-503.

  • [35] Miskiewicz J. Szachniuk M. Discovering structural motifs in miRNA precursors from Viridiplantae kingdom Molecules23 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 Proteins86 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 Research42 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 Research39 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 RNA15 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 America85 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 Chemistry3 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 Research36 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 Bioinformatics11 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 Research40 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 Bioinformatics28 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 Riboswitches553 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 Research41 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 Bioinformatics16 2015 276.

  • [49] Seetin M.G. Mathews D.H. RNA structure prediction: an overview of methods Methods of Molecular Biology905 2012 99-122.

  • [50] Stevens R.D. Robinson A.J. Goble C.A. MyGrid: Personalised bioinformatics on the information grid Bioinformatics19 2003 i302-i304.

  • [51] Sugawara H. Ogasawara O. Okubo K. Gojobori T. Tateno Y. Ddbj with new system and face Nucleic Acids Research36 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 Bioinformatics18 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 Sciences41 2016 123-142.

  • [56] wwPDB consortium Protein Data Bank: the single global archive for 3D macromolecular structure data Nucleic Acids Research47 2019 D520–D528.

  • [57] Zok T. Popenda M. Szachniuk M. MCQ4Structures to compute similarity of molecule structures Central European Journal of Operations Research22 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 Research46 2018 W30-W35.

Journal information
Impact Factor

CiteScore 2018: 0.61

SCImago Journal Rank (SJR) 2018: 0.152
Source Normalized Impact per Paper (SNIP) 2018: 0.463

Mathematical Citation Quotient (MCQ) 2018: 0.08

Cited By
All Time Past Year Past 30 Days
Abstract Views 0 0 0
Full Text Views 279 279 17
PDF Downloads 209 209 12