Nucleic acid structure prediction (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "Nucleic acid structure prediction" in English language version.

refsWebsite

Global rank English rank

65nih.gov

4^th place

43doi.org

2^nd place

10worldcat.org

5^th place

6harvard.edu

18^th place

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5semanticscholar.org

11^th place

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3psu.edu

207^th place

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2arxiv.org

69^th place

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2biomedcentral.com

2,747^th place

7,129^th place

1ucl.ac.uk

1,306^th place

885^th place

1handle.net

102^nd place

76^th place

arxiv.org (Global: 69^th place; English: 59^th place)

Rivas E, Eddy SR (1999). "A dynamic programming algorithm for RNA structure prediction including pseudoknots". J Mol Biol. 285 (5): 2053–68. arXiv:physics/9807048. doi:10.1006/jmbi.1998.2436. PMID 9925784. S2CID 2228845.
Malik, A; Zhang, L; Gautam, M; Dai, N; Li, S; Zhang, H; Mathews, DH; Huang, L (1 September 2024). "LinearAlifold: Linear-time consensus structure prediction for RNA alignments". Journal of Molecular Biology. 436 (17) 168694. arXiv:2206.14794. doi:10.1016/j.jmb.2024.168694. PMC 11377157. PMID 38971557.

biomedcentral.com (Global: 2,747^th place; English: 7,129^th place)

Harmanci AO, Sharma G, Mathews DH, (2007), Efficient Pairwise RNA Structure Prediction Using Probabilistic Alignment Constraints in Dynalign, BMC Bioinformatics, 8(130).
Holmes I. (2005) Accelerated probabilistic inference of RNA structure evolution. BMC Bioinformatics. 2005 Mar 24;6:73.

doi.org (Global: 2^nd place; English: 2^nd place)

Ponce-Salvatierra, Almudena; Astha; Merdas, Katarzyna; Chandran, Nithin; Ghosh, Pritha; Mukherjee, Sunandan; Bujnicki, Janusz M (2019-01-22). "Computational modeling of RNA 3D structure based on experimental data". Bioscience Reports. 39 (2) BSR20180430. doi:10.1042/bsr20180430. ISSN 0144-8463. PMC 6367127. PMID 30670629.
Magnus, Marcin; Matelska, Dorota; Łach, Grzegorz; Chojnowski, Grzegorz; Boniecki, Michal J; Purta, Elzbieta; Dawson, Wayne; Dunin-Horkawicz, Stanislaw; Bujnicki, Janusz M (2014-04-23). "Computational modeling of RNA 3D structures, with the aid of experimental restraints". RNA Biology. 11 (5): 522–536. doi:10.4161/rna.28826. ISSN 1547-6286. PMC 4152360. PMID 24785264.
Mathews D.H. (2006). "Revolutions in RNA secondary structure prediction". J. Mol. Biol. 359 (3): 526–532. doi:10.1016/j.jmb.2006.01.067. PMID 16500677.
Mathews DH, Sabina J, Zuker M, Turner DH (1999). "Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure". J Mol Biol. 288 (5): 911–40. doi:10.1006/jmbi.1999.2700. PMID 10329189. S2CID 19989405.
Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, Turner DH (2004). "Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure". Proceedings of the National Academy of Sciences USA. 101 (19): 7287–7292. Bibcode:2004PNAS..101.7287M. doi:10.1073/pnas.0401799101. PMC 409911. PMID 15123812.
Andronescu, M; Condon, A; Hoos, HH; Mathews, DH; Murphy, KP (1 July 2007). "Efficient parameter estimation for RNA secondary structure prediction". Bioinformatics. 23 (13): i19-28. doi:10.1093/bioinformatics/btm223. PMID 17646296.
Chou, Fang-Chieh; Kladwang, Wipapat; Kappel, Kalli; Das, Rhiju (26 July 2016). "Blind tests of RNA nearest-neighbor energy prediction". Proceedings of the National Academy of Sciences of the United States of America. 113 (30): 8430–5. Bibcode:2016PNAS..113.8430C. doi:10.1073/pnas.1523335113. PMC 4968729. PMID 27402765.
Langdon, William B.; Petke, Justyna; Lorenz, Ronny (2018). "Evolving Better RNAfold Structure Prediction". Genetic Programming. Lecture Notes in Computer Science. Vol. 10781. pp. 220–236. doi:10.1007/978-3-319-77553-1_14. ISBN 978-3-319-77552-4.
Raden, Martin; Müller, Teresa; Mautner, Stefan; Gelhausen, Rick; Backofen, Rolf (December 2020). "The impact of various seed, accessibility and interaction constraints on sRNA target prediction- a systematic assessment". BMC Bioinformatics. 21 (1): 15. doi:10.1186/s12859-019-3143-4. PMC 6956497. PMID 31931703.
Zuker M.; Sankoff D. (1984). "RNA secondary structures and their prediction". Bull. Math. Biol. 46 (4): 591–621. doi:10.1016/s0092-8240(84)80062-2 (inactive 1 July 2025). S2CID 189885784.{{cite journal}}: CS1 maint: DOI inactive as of July 2025 (link)
Nussinov R, Jacobson AB (1980). "Fast algorithm for predicting the secondary structure of single-stranded RNA". Proc Natl Acad Sci U S A. 77 (11): 6309–13. Bibcode:1980PNAS...77.6309N. doi:10.1073/pnas.77.11.6309. PMC 350273. PMID 6161375.
Zuker M, Stiegler P (1981). "Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information". Nucleic Acids Res. 9 (1): 133–48. doi:10.1093/nar/9.1.133. PMC 326673. PMID 6163133.
Rivas E, Eddy SR (1999). "A dynamic programming algorithm for RNA structure prediction including pseudoknots". J Mol Biol. 285 (5): 2053–68. arXiv:physics/9807048. doi:10.1006/jmbi.1998.2436. PMID 9925784. S2CID 2228845.
Reeder J.; Giegerich R. (2004). "Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics". BMC Bioinformatics. 5 104. doi:10.1186/1471-2105-5-104. PMC 514697. PMID 15294028.
Lyngsø RB, Pedersen CN (2000). "RNA pseudoknot prediction in energy-based models". J Comput Biol. 7 (3–4): 409–427. CiteSeerX 10.1.1.34.4044. doi:10.1089/106652700750050862. PMID 11108471.
- Varenyk, Yuliia; Spicher, Thomas; Hofacker, Ivo L; Lorenz, Ronny (1 November 2023). "Modified RNAs and predictions with the ViennaRNA Package". Bioinformatics. 39 (11) btad696. doi:10.1093/bioinformatics/btad696. PMC 10676514. PMID 37971965.
- Zuker M (2003). "Mfold web server for nucleic acid folding and hybridization prediction". Nucleic Acids Research. 31 (13): 3406–3415. doi:10.1093/nar/gkg595. PMC 169194. PMID 12824337.
- McCaskill JS (1990). "The equilibrium partition function and base pair binding probabilities for RNA secondary structure". Biopolymers. 29 (6–7): 1105–19. doi:10.1002/bip.360290621. hdl:11858/00-001M-0000-0013-0DE3-9. PMID 1695107. S2CID 12629688.
- Ding Y, Lawrence CE (2003). "A statistical sampling algorithm for RNA secondary structure prediction". Nucleic Acids Res. 31 (24): 7280–301. doi:10.1093/nar/gkg938. PMC 297010. PMID 14654704.
- Gardner P.P.; Giegerich, Robert (2004). "A comprehensive comparison of comparative RNA structure prediction approaches". BMC Bioinformatics. 5 140. doi:10.1186/1471-2105-5-140. PMC 526219. PMID 15458580.
- Bernhart SH, Hofacker IL (2009). "From consensus structure prediction to RNA gene finding". Brief Funct Genomic Proteomic. 8 (6): 461–71. doi:10.1093/bfgp/elp043. PMID 19833701.
- Knudsen B, Hein J (2003). "Pfold: RNA secondary structure prediction using stochastic context-free grammars". Nucleic Acids Res. 31 (13): 3423–8. doi:10.1093/nar/gkg614. PMC 169020. PMID 12824339.
- Hofacker IL, Fekete M, Stadler PF (2002). "Secondary structure prediction for aligned RNA sequences". J Mol Biol. 319 (5): 1059–66. CiteSeerX 10.1.1.73.479. doi:10.1016/S0022-2836(02)00308-X. PMID 12079347.
- Malik, A; Zhang, L; Gautam, M; Dai, N; Li, S; Zhang, H; Mathews, DH; Huang, L (1 September 2024). "LinearAlifold: Linear-time consensus structure prediction for RNA alignments". Journal of Molecular Biology. 436 (17) 168694. arXiv:2206.14794. doi:10.1016/j.jmb.2024.168694. PMC 11377157. PMID 38971557.
- Siebert, S; Backofen, R (15 August 2005). "MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons". Bioinformatics. 21 (16): 3352–9. doi:10.1093/bioinformatics/bti550. PMID 15972285.
- Sankoff D (1985). "Simultaneous solution of the RNA folding, alignment and protosequence problems". SIAM Journal on Applied Mathematics. 45 (5): 810–825. CiteSeerX 10.1.1.665.4890. doi:10.1137/0145048.
- Hofacker IL, Bernhart SH, Stadler PF (2004). "Alignment of RNA base pairing probability matrices". Bioinformatics. 20 (14): 2222–7. doi:10.1093/bioinformatics/bth229. PMID 15073017.
- Havgaard JH, Lyngso RB, Stormo GD, Gorodkin J (2005). "Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%". Bioinformatics. 21 (9): 1815–24. doi:10.1093/bioinformatics/bti279. PMID 15657094.
- Mathews DH, Turner DH (2002). "Dynalign: an algorithm for finding the secondary structure common to two RNA sequences". J Mol Biol. 317 (2): 191–203. doi:10.1006/jmbi.2001.5351. PMID 11902836.
- Kiryu H, Tabei Y, Kin T, Asai K (2007). "Murlet: A practical multiple alignment tool for structural RNA sequences". Bioinformatics. 23 (13): 1588–1598. doi:10.1093/bioinformatics/btm146. PMID 17459961.
- Will, S; Joshi, T; Hofacker, IL; Stadler, PF; Backofen, R (May 2012). "LocARNA-P: accurate boundary prediction and improved detection of structural RNAs". RNA. 18 (5): 900–14. doi:10.1261/rna.029041.111. PMC 3334699. PMID 22450757.
- Sorescu, DA; Möhl, M; Mann, M; Backofen, R; Will, S (July 2012). "CARNA--alignment of RNA structure ensembles". Nucleic Acids Research. 40 (Web Server issue): W49-53. doi:10.1093/nar/gks491. PMC 3394245. PMID 22689637.
- Major F, Turcotte M, Gautheret D, Lapalme G, Fillion E, Cedergren R (Sep 1991). "The combination of symbolic and numerical computation for three-dimensional modeling of RNA". Science. 253 (5025): 1255–60. Bibcode:1991Sci...253.1255F. doi:10.1126/science.1716375. PMID 1716375.
- Major F, Gautheret D, Cedergren R (Oct 1993). "Reproducing the three-dimensional structure of a tRNA molecule from structural constraints". Proc Natl Acad Sci U S A. 90 (20): 9408–12. Bibcode:1993PNAS...90.9408M. doi:10.1073/pnas.90.20.9408. PMC 47577. PMID 8415714.
- Frellsen J, Moltke I, Thiim M, Mardia KV, Ferkinghoff-Borg J, Hamelryck T (2009). "A probabilistic model of RNA conformational space". PLOS Comput Biol. 5 (6) e1000406. Bibcode:2009PLSCB...5E0406F. doi:10.1371/journal.pcbi.1000406. PMC 2691987. PMID 19543381.
- Rother, Magdalena; Rother, Kristian; Puton, Tomasz; Bujnicki, Janusz M. (2011-02-07). "ModeRNA: a tool for comparative modeling of RNA 3D structure". Nucleic Acids Research. 39 (10): 4007–4022. doi:10.1093/nar/gkq1320. ISSN 1362-4962. PMC 3105415. PMID 21300639.
- Zhao, Chenhan; Xu, Xiaojun; Chen, Shi-Jie (2017), "Predicting RNA Structure with Vfold", Functional Genomics, Methods in Molecular Biology, vol. 1654, Springer New York, pp. 3–15, doi:10.1007/978-1-4939-7231-9_1, ISBN 978-1-4939-7230-2, PMC 5762135, PMID 28986779
- Vangaveti, Sweta; Ranganathan, Srivathsan V.; Chen, Alan A. (2016-10-04). "Advances in RNA molecular dynamics: a simulator's guide to RNA force fields". Wiley Interdisciplinary Reviews: RNA. 8 (2) e1396. doi:10.1002/wrna.1396. ISSN 1757-7004. PMID 27704698. S2CID 35501632.
- Chen, Shi-Jie (June 2008). "RNA Folding: Conformational Statistics, Folding Kinetics, and Ion Electrostatics". Annual Review of Biophysics. 37 (1): 197–214. doi:10.1146/annurev.biophys.37.032807.125957. ISSN 1936-122X. PMC 2473866. PMID 18573079.
- Laing, Christian; Schlick, Tamar (June 2011). "Computational approaches to RNA structure prediction, analysis, and design". Current Opinion in Structural Biology. 21 (3): 306–318. doi:10.1016/j.sbi.2011.03.015. ISSN 0959-440X. PMC 3112238. PMID 21514143.
- Boniecki, Michal J.; Lach, Grzegorz; Dawson, Wayne K.; Tomala, Konrad; Lukasz, Pawel; Soltysinski, Tomasz; Rother, Kristian M.; Bujnicki, Janusz M. (2015-12-19). "SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction". Nucleic Acids Research. 44 (7): e63. doi:10.1093/nar/gkv1479. ISSN 0305-1048. PMC 4838351. PMID 26687716.
- Stasiewicz, Juliusz; Mukherjee, Sunandan; Nithin, Chandran; Bujnicki, Janusz M. (2019-03-21). "QRNAS: software tool for refinement of nucleic acid structures". BMC Structural Biology. 19 (1): 5. doi:10.1186/s12900-019-0103-1. ISSN 1472-6807. PMC 6429776. PMID 30898165.
- Nithin, Chandran; Kmiecik, Sebastian; Błaszczyk, Roman; Nowicka, Julita; Tuszyńska, Irina (2024-06-25). "Comparative analysis of RNA 3D structure prediction methods: towards enhanced modeling of RNA–ligand interactions". Nucleic Acids Research. 52 (13): 7465–7486. doi:10.1093/nar/gkae541. ISSN 0305-1048. PMC 11260495. PMID 38917327.
handle.net (Global: 102^nd place; English: 76^th place)
hdl.handle.net
- McCaskill JS (1990). "The equilibrium partition function and base pair binding probabilities for RNA secondary structure". Biopolymers. 29 (6–7): 1105–19. doi:10.1002/bip.360290621. hdl:11858/00-001M-0000-0013-0DE3-9. PMID 1695107. S2CID 12629688.
harvard.edu (Global: 18^th place; English: 17^th place)
ui.adsabs.harvard.edu
- Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, Turner DH (2004). "Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure". Proceedings of the National Academy of Sciences USA. 101 (19): 7287–7292. Bibcode:2004PNAS..101.7287M. doi:10.1073/pnas.0401799101. PMC 409911. PMID 15123812.
- Chou, Fang-Chieh; Kladwang, Wipapat; Kappel, Kalli; Das, Rhiju (26 July 2016). "Blind tests of RNA nearest-neighbor energy prediction". Proceedings of the National Academy of Sciences of the United States of America. 113 (30): 8430–5. Bibcode:2016PNAS..113.8430C. doi:10.1073/pnas.1523335113. PMC 4968729. PMID 27402765.
- Nussinov R, Jacobson AB (1980). "Fast algorithm for predicting the secondary structure of single-stranded RNA". Proc Natl Acad Sci U S A. 77 (11): 6309–13. Bibcode:1980PNAS...77.6309N. doi:10.1073/pnas.77.11.6309. PMC 350273. PMID 6161375.
- Major F, Turcotte M, Gautheret D, Lapalme G, Fillion E, Cedergren R (Sep 1991). "The combination of symbolic and numerical computation for three-dimensional modeling of RNA". Science. 253 (5025): 1255–60. Bibcode:1991Sci...253.1255F. doi:10.1126/science.1716375. PMID 1716375.
- Major F, Gautheret D, Cedergren R (Oct 1993). "Reproducing the three-dimensional structure of a tRNA molecule from structural constraints". Proc Natl Acad Sci U S A. 90 (20): 9408–12. Bibcode:1993PNAS...90.9408M. doi:10.1073/pnas.90.20.9408. PMC 47577. PMID 8415714.
- Frellsen J, Moltke I, Thiim M, Mardia KV, Ferkinghoff-Borg J, Hamelryck T (2009). "A probabilistic model of RNA conformational space". PLOS Comput Biol. 5 (6) e1000406. Bibcode:2009PLSCB...5E0406F. doi:10.1371/journal.pcbi.1000406. PMC 2691987. PMID 19543381.
nih.gov (Global: 4^th place; English: 4^th place)
pubmed.ncbi.nlm.nih.gov
- Ponce-Salvatierra, Almudena; Astha; Merdas, Katarzyna; Chandran, Nithin; Ghosh, Pritha; Mukherjee, Sunandan; Bujnicki, Janusz M (2019-01-22). "Computational modeling of RNA 3D structure based on experimental data". Bioscience Reports. 39 (2) BSR20180430. doi:10.1042/bsr20180430. ISSN 0144-8463. PMC 6367127. PMID 30670629.
- Magnus, Marcin; Matelska, Dorota; Łach, Grzegorz; Chojnowski, Grzegorz; Boniecki, Michal J; Purta, Elzbieta; Dawson, Wayne; Dunin-Horkawicz, Stanislaw; Bujnicki, Janusz M (2014-04-23). "Computational modeling of RNA 3D structures, with the aid of experimental restraints". RNA Biology. 11 (5): 522–536. doi:10.4161/rna.28826. ISSN 1547-6286. PMC 4152360. PMID 24785264.
- Mathews D.H. (2006). "Revolutions in RNA secondary structure prediction". J. Mol. Biol. 359 (3): 526–532. doi:10.1016/j.jmb.2006.01.067. PMID 16500677.
- Mathews DH, Sabina J, Zuker M, Turner DH (1999). "Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure". J Mol Biol. 288 (5): 911–40. doi:10.1006/jmbi.1999.2700. PMID 10329189. S2CID 19989405.
- Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, Turner DH (2004). "Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure". Proceedings of the National Academy of Sciences USA. 101 (19): 7287–7292. Bibcode:2004PNAS..101.7287M. doi:10.1073/pnas.0401799101. PMC 409911. PMID 15123812.
- Andronescu, M; Condon, A; Hoos, HH; Mathews, DH; Murphy, KP (1 July 2007). "Efficient parameter estimation for RNA secondary structure prediction". Bioinformatics. 23 (13): i19-28. doi:10.1093/bioinformatics/btm223. PMID 17646296.
- Chou, Fang-Chieh; Kladwang, Wipapat; Kappel, Kalli; Das, Rhiju (26 July 2016). "Blind tests of RNA nearest-neighbor energy prediction". Proceedings of the National Academy of Sciences of the United States of America. 113 (30): 8430–5. Bibcode:2016PNAS..113.8430C. doi:10.1073/pnas.1523335113. PMC 4968729. PMID 27402765.
- Raden, Martin; Müller, Teresa; Mautner, Stefan; Gelhausen, Rick; Backofen, Rolf (December 2020). "The impact of various seed, accessibility and interaction constraints on sRNA target prediction- a systematic assessment". BMC Bioinformatics. 21 (1): 15. doi:10.1186/s12859-019-3143-4. PMC 6956497. PMID 31931703.
- Nussinov R, Jacobson AB (1980). "Fast algorithm for predicting the secondary structure of single-stranded RNA". Proc Natl Acad Sci U S A. 77 (11): 6309–13. Bibcode:1980PNAS...77.6309N. doi:10.1073/pnas.77.11.6309. PMC 350273. PMID 6161375.
- Zuker M, Stiegler P (1981). "Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information". Nucleic Acids Res. 9 (1): 133–48. doi:10.1093/nar/9.1.133. PMC 326673. PMID 6163133.
- Rivas E, Eddy SR (1999). "A dynamic programming algorithm for RNA structure prediction including pseudoknots". J Mol Biol. 285 (5): 2053–68. arXiv:physics/9807048. doi:10.1006/jmbi.1998.2436. PMID 9925784. S2CID 2228845.
- Reeder J.; Giegerich R. (2004). "Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics". BMC Bioinformatics. 5 104. doi:10.1186/1471-2105-5-104. PMC 514697. PMID 15294028.
- Lyngsø RB, Pedersen CN (2000). "RNA pseudoknot prediction in energy-based models". J Comput Biol. 7 (3–4): 409–427. CiteSeerX 10.1.1.34.4044. doi:10.1089/106652700750050862. PMID 11108471.
- - Varenyk, Yuliia; Spicher, Thomas; Hofacker, Ivo L; Lorenz, Ronny (1 November 2023). "Modified RNAs and predictions with the ViennaRNA Package". Bioinformatics. 39 (11) btad696. doi:10.1093/bioinformatics/btad696. PMC 10676514. PMID 37971965.
  - Zuker M (2003). "Mfold web server for nucleic acid folding and hybridization prediction". Nucleic Acids Research. 31 (13): 3406–3415. doi:10.1093/nar/gkg595. PMC 169194. PMID 12824337.
  - McCaskill JS (1990). "The equilibrium partition function and base pair binding probabilities for RNA secondary structure". Biopolymers. 29 (6–7): 1105–19. doi:10.1002/bip.360290621. hdl:11858/00-001M-0000-0013-0DE3-9. PMID 1695107. S2CID 12629688.
  - Ding Y, Lawrence CE (2003). "A statistical sampling algorithm for RNA secondary structure prediction". Nucleic Acids Res. 31 (24): 7280–301. doi:10.1093/nar/gkg938. PMC 297010. PMID 14654704.
  - Gardner P.P.; Giegerich, Robert (2004). "A comprehensive comparison of comparative RNA structure prediction approaches". BMC Bioinformatics. 5 140. doi:10.1186/1471-2105-5-140. PMC 526219. PMID 15458580.
  - Bernhart SH, Hofacker IL (2009). "From consensus structure prediction to RNA gene finding". Brief Funct Genomic Proteomic. 8 (6): 461–71. doi:10.1093/bfgp/elp043. PMID 19833701.
  - Knudsen B, Hein J (2003). "Pfold: RNA secondary structure prediction using stochastic context-free grammars". Nucleic Acids Res. 31 (13): 3423–8. doi:10.1093/nar/gkg614. PMC 169020. PMID 12824339.
  - Hofacker IL, Fekete M, Stadler PF (2002). "Secondary structure prediction for aligned RNA sequences". J Mol Biol. 319 (5): 1059–66. CiteSeerX 10.1.1.73.479. doi:10.1016/S0022-2836(02)00308-X. PMID 12079347.
  - Malik, A; Zhang, L; Gautam, M; Dai, N; Li, S; Zhang, H; Mathews, DH; Huang, L (1 September 2024). "LinearAlifold: Linear-time consensus structure prediction for RNA alignments". Journal of Molecular Biology. 436 (17) 168694. arXiv:2206.14794. doi:10.1016/j.jmb.2024.168694. PMC 11377157. PMID 38971557.
  - Siebert, S; Backofen, R (15 August 2005). "MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons". Bioinformatics. 21 (16): 3352–9. doi:10.1093/bioinformatics/bti550. PMID 15972285.
  - Hofacker IL, Bernhart SH, Stadler PF (2004). "Alignment of RNA base pairing probability matrices". Bioinformatics. 20 (14): 2222–7. doi:10.1093/bioinformatics/bth229. PMID 15073017.
  - Havgaard JH, Lyngso RB, Stormo GD, Gorodkin J (2005). "Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%". Bioinformatics. 21 (9): 1815–24. doi:10.1093/bioinformatics/bti279. PMID 15657094.
  - Mathews DH, Turner DH (2002). "Dynalign: an algorithm for finding the secondary structure common to two RNA sequences". J Mol Biol. 317 (2): 191–203. doi:10.1006/jmbi.2001.5351. PMID 11902836.
  - Kiryu H, Tabei Y, Kin T, Asai K (2007). "Murlet: A practical multiple alignment tool for structural RNA sequences". Bioinformatics. 23 (13): 1588–1598. doi:10.1093/bioinformatics/btm146. PMID 17459961.
  - Will, S; Joshi, T; Hofacker, IL; Stadler, PF; Backofen, R (May 2012). "LocARNA-P: accurate boundary prediction and improved detection of structural RNAs". RNA. 18 (5): 900–14. doi:10.1261/rna.029041.111. PMC 3334699. PMID 22450757.
  - Sorescu, DA; Möhl, M; Mann, M; Backofen, R; Will, S (July 2012). "CARNA--alignment of RNA structure ensembles". Nucleic Acids Research. 40 (Web Server issue): W49-53. doi:10.1093/nar/gks491. PMC 3394245. PMID 22689637.
  - Major F, Turcotte M, Gautheret D, Lapalme G, Fillion E, Cedergren R (Sep 1991). "The combination of symbolic and numerical computation for three-dimensional modeling of RNA". Science. 253 (5025): 1255–60. Bibcode:1991Sci...253.1255F. doi:10.1126/science.1716375. PMID 1716375.
  - Major F, Gautheret D, Cedergren R (Oct 1993). "Reproducing the three-dimensional structure of a tRNA molecule from structural constraints". Proc Natl Acad Sci U S A. 90 (20): 9408–12. Bibcode:1993PNAS...90.9408M. doi:10.1073/pnas.90.20.9408. PMC 47577. PMID 8415714.
  - Frellsen J, Moltke I, Thiim M, Mardia KV, Ferkinghoff-Borg J, Hamelryck T (2009). "A probabilistic model of RNA conformational space". PLOS Comput Biol. 5 (6) e1000406. Bibcode:2009PLSCB...5E0406F. doi:10.1371/journal.pcbi.1000406. PMC 2691987. PMID 19543381.
  - Rother, Magdalena; Rother, Kristian; Puton, Tomasz; Bujnicki, Janusz M. (2011-02-07). "ModeRNA: a tool for comparative modeling of RNA 3D structure". Nucleic Acids Research. 39 (10): 4007–4022. doi:10.1093/nar/gkq1320. ISSN 1362-4962. PMC 3105415. PMID 21300639.
  - Zhao, Chenhan; Xu, Xiaojun; Chen, Shi-Jie (2017), "Predicting RNA Structure with Vfold", Functional Genomics, Methods in Molecular Biology, vol. 1654, Springer New York, pp. 3–15, doi:10.1007/978-1-4939-7231-9_1, ISBN 978-1-4939-7230-2, PMC 5762135, PMID 28986779
  - Vangaveti, Sweta; Ranganathan, Srivathsan V.; Chen, Alan A. (2016-10-04). "Advances in RNA molecular dynamics: a simulator's guide to RNA force fields". Wiley Interdisciplinary Reviews: RNA. 8 (2) e1396. doi:10.1002/wrna.1396. ISSN 1757-7004. PMID 27704698. S2CID 35501632.
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    Laing, Christian; Schlick, Tamar (June 2011). "Computational approaches to RNA structure prediction, analysis, and design". Current Opinion in Structural Biology. 21 (3): 306–318. doi:10.1016/j.sbi.2011.03.015. ISSN 0959-440X. PMC 3112238. PMID 21514143.
    Boniecki, Michal J.; Lach, Grzegorz; Dawson, Wayne K.; Tomala, Konrad; Lukasz, Pawel; Soltysinski, Tomasz; Rother, Kristian M.; Bujnicki, Janusz M. (2015-12-19). "SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction". Nucleic Acids Research. 44 (7): e63. doi:10.1093/nar/gkv1479. ISSN 0305-1048. PMC 4838351. PMID 26687716.
    Stasiewicz, Juliusz; Mukherjee, Sunandan; Nithin, Chandran; Bujnicki, Janusz M. (2019-03-21). "QRNAS: software tool for refinement of nucleic acid structures". BMC Structural Biology. 19 (1): 5. doi:10.1186/s12900-019-0103-1. ISSN 1472-6807. PMC 6429776. PMID 30898165.
    Nithin, Chandran; Kmiecik, Sebastian; Błaszczyk, Roman; Nowicka, Julita; Tuszyńska, Irina (2024-06-25). "Comparative analysis of RNA 3D structure prediction methods: towards enhanced modeling of RNA–ligand interactions". Nucleic Acids Research. 52 (13): 7465–7486. doi:10.1093/nar/gkae541. ISSN 0305-1048. PMC 11260495. PMID 38917327.
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