RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction

RNA

Volumn 18, Issue 4, 2012, Pages 610-625

  Cruz, José Almeida ^a   Blanchet, Marc Frédérick ^b   Boniecki, Michal ^c   Bujnicki, Janusz M ^c,d   Chen, Shi Jie ^e   Cao, Song ^e   Das, Rhiju ^f   Ding, Feng ^g   Dokholyan, Nikolay V ^g   Flores, Samuel Coulbourn ^h   Huang, Lili ⁱ   Lavender, Christopher A ^j   Lisi, Véronique ^b   Major, François ^b   Mikolajczak, Katarzyna ^c   Patel, Dinshaw J ⁱ   Philips, Anna ^c,d   Puton, Tomasz ^d   Santalucia, John ^k,l   Sijenyi, Fredrick ^l   Hermann, Thomas ^m   Rother, Kristian ^d   Rother, Magdalena ^d   Serganov, Alexander ⁱ   Skorupski, Marcin ^d   Soltysinski, Tomasz ^c   Sripakdeevong, Parin ^f   Tuszynska, Irina ^c   Weeks, Kevin M ^j   Waldsich, Christina ⁿ   Wildauer, Michael ⁿ   Leontis, Neocles B ^o   Westhof, Eric ^a   more..

^a UNIVERSITÉ DE STRASBOURG   (France)

^b INSTITUTE FOR RESEARCH IN IMMUNOLOGY AND CANCER   (Canada)

^c INTERNATIONAL INSTITUTE OF MOLECULAR AND CELL BIOLOGY   (Poland)

^d ADAM MICKIEWICZ UNIVERSITY   (Poland)

^e University of Missouri   (United States)

^f STANFORD UNIVERSITY   (United States)

^g UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

^h UPPSALA UNIVERSITY   (Sweden)

ⁱ MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^j University of North Carolina at Chapel Hill   (United States)

^k WAYNE STATE UNIVERSITY   (United States)

^l DNA Software   (United States)

^m UNIVERSITY OF CALIFORNIA   (United States)

ⁿ UNIVERSITY OF VIENNA   (Austria)

^o BOWLING GREEN STATE UNIVERSITY   (United States)

more..

Author keywords

3D prediction; Bioinformatics; Force fields; Structure

Indexed keywords

ARTICLE; BASE PAIRING; CONTROLLED STUDY; PRIORITY JOURNAL; PROTEIN FOLDING; RNA ANALYSIS; RNA SEQUENCE; RNA STRUCTURE; SEQUENCE ANALYSIS;

BASE SEQUENCE; DIMERIZATION; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RNA;

EID: 84863338065     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.031054.111     Document Type: Article

References (70)

1. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. 2000. The Protein Data Bank. Nucleic Acids Res 28: 235-242. (Pubitemid 30047768)
2. Berry KE, Waghray S, Mortimer SA, Bai Y, Doudna JA. 2011. Crystal structure of the HCV IRES central domain reveals strategy for start-codon positioning. Structure 19: 1456-1466.
3. Boniecki M, Rotkiewicz P, Skolnick J, Kolinski A. 2003. Protein fragment reconstruction using various modeling techniques. J Comput Aided Mol Des 17: 725-738. (Pubitemid 38418285)
4. Cao S, Chen S-J. 2005. Predicting RNA folding thermodynamics with a reduced chain representation model. RNA 11: 1884-1897. (Pubitemid 41720037)
5. Cao S, Chen S-J. 2006a. Predicting RNA pseudoknot folding thermodynamics. Nucleic Acids Res 34: 2634-2652. (Pubitemid 43985627)
6. Cao S, Chen S-J. 2006b. Free energy landscapes of RNA/RNA complexes: With applications to snRNA complexes in spliceosomes. J Mol Biol 357: 292-312. (Pubitemid 43339332)
7. Cao S, Chen S-J. 2009. Predicting structures and stabilities for H-type pseudoknots with interhelix loops. RNA 15: 696-706.
8. Cao S, Chen S-J. 2011. Physics-based de novo prediction of RNA 3D structures. J Phys Chem B 115: 4216-4226.
9. Chen S-J. 2008. RNA folding: Conformational statistics, folding kinetics, and ion electrostatics. Annu Rev Biophys 37: 197-214.
10. Cruz JA, Westhof E. 2011. Sequence-based identification of 3D structural modules in RNA with RMDetect. Nat Methods 8: 513-519.
11. Darty K, Denise A, Ponty Y. 2009. VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics 25: 1974-1975.
12. Das R, Baker D. 2008. Macromolecular modeling with rosetta. Annu Rev Biochem 77: 363-382.
13. Das R, Karanicolas J, Baker D. 2010. Atomic accuracy in predicting and designing noncanonical RNA structure. Nat Methods 7: 291-294.
14. Davis IW, Leaver-Fay A, Chen VB, Block JN, Kapral GJ, Wang X, Murray LW, Arendall WB III, Snoeyink J, Richardson JS, et al. 2007. MolProbity: All-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res 35: W375-W383. doi: 10.1093/nar/gkm216.
15. Dibrov S, McLean J, Hermann T. 2011a. Structure of an RNA dimer of a regulatory element from human thymidylate synthase mRNA. Acta Crystallogr D Biol Crystallogr 67: 97-104.
16. Dibrov SM, McLean J, Parsons J, Hermann T. 2011b. Self-assembling RNA square. Proc Natl Acad Sci 108: 6405-6408.
17. Ding F, Dokholyan N. 2012. Multiscale modeling of RNA structure and dynamics. In RNA 3D structure analysis and prediction (ed. NB Leontis, E Westhof). Springer-Verlag, Berlin.
18. Ding F, Tsao D, Nie H, Dokholyan N. 2008a. Ab initio folding of proteins using all-atom discrete molecular dynamics. Structure 16: 1010-1018. (Pubitemid 351899281)
19. Ding F, Sharma S, Chalasani P, Demidov VV, Broude NE, Dokholyan NV. 2008b. Ab initio RNA folding by discrete molecular dynamics: From structure prediction to folding mechanisms. RNA 14: 1164-1173. (Pubitemid 351717496)
20. Ditzler MA, Otyepka M, Sponer J, Walter NG. 2010. Molecular dynamics and quantum mechanics of RNA: Conformational and chemical change we can believe in. Acc Chem Res 43: 40-47.
21. Flores SC, Altman RB. 2010. Turning limited experimental information into 3D models of RNA. RNA 16: 1769-1778.
22. Flores SC, Altman R. 2011. Structural insights into pre-translocation ribosome motions. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 205-11. http://www.ncbi.nlm.nih. gov/pubmed/21121048.
23. Flores SC, Wan Y, Russell R, Altman RB. 2010. Predicting RNA structure by multiple template homology modeling. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 216-27. http:// www.pubmedcentral.nih.gov/ articlerender.fcgi?artid=2872935&tool= pmcentrez&rendertype=abstract.
24. Flores SC, Sherman MA, Bruns CM, Eastman P, Altman RB. 2011. Fast flexible modeling of RNA structure using internal coordinates. IEEE/ACM Trans Comput Biol Bioinformatics 8: 1247-1257.
25. Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S, Wilkinson AC, Finn RD, Griffiths-Jones S, Eddy SR, et al. 2009. Rfam: Updates to the RNA families database. Nucleic Acids Res 37: D136-D140. doi: 10.1093/nar/gkn766.
26. Gendron P, Lemieux S, Major F. 2001. Quantitative analysis of nucleic acid three-dimensional structures. J Mol Biol 308: 919-936. (Pubitemid 32574369)
27. Gherghe CM, Leonard CW, Ding F, Dokholyan NV, Weeks KM. 2009. Native-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular dynamics. J Am Chem Soc 131: 2541-2546.
28. Golub G, Van Loan C. 1989. Matrix computations. Johns Hopkins University Press, Baltimore.
29. Hajdin CE, Ding F, Dokholyan NV, Weeks KM. 2010. On the significance of an RNA tertiary structure prediction. RNA 16: 1340-1349.
30. Hamelryck T. 2003. PDB file parser and structure class implemented in Python. Bioinformatics 19: 2308-2310. (Pubitemid 37483987)
31. Hofacker IL, Fontana W, Stadler PF, Bonhoeffer LS, Tacker M, Schuster P. 1994. Fast folding and comparison of RNA secondary structures. Monatsh Chem 125: 167-188.
32. Huang L, Serganov A, Patel DJ. 2010. Structural insights into ligand recognition by a sensing domain of the cooperative glycine riboswitch. Mol Cell 40: 774-786.
33. Jonikas MA, Radmer RJ, Altman RB. 2009. Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models. Bioinformatics 25: 3259-3266.
34. Jossinet F, Ludwig TE, Westhof E. 2010. Assemble: An interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels. Bioinformatics 26: 2057-2059.
35. Kosinski J, Cymerman IA, Feder M, Kurowski MA, Sasin JM, Bujnicki JM. 2003. A "FRankenstein's monster" approach to comparative modeling: Merging the finest fragments of Fold-Recognition models and iterative model refinement aided by 3D structure evaluation. Proteins 53: 369-379. (Pubitemid 37352195)
36. Lavender CA, Ding F, Dokholyan NV, Weeks KM. 2010. Robust and generic RNA modeling using inferred constraints: A structure for the hepatitis C virus IRES pseudoknot domain. Biochemistry 49: 4931-4933.
37. Leontis NB, Westhof E. 2001. Geometric nomenclature and classification of RNA base pairs. RNA 7: 499-512. (Pubitemid 32416808)
38. Leontis NB, Stombaugh J, Westhof E. 2002. The non-Watson-Crick base pairs and their associated isostericity matrices. Nucleic Acids Res 30: 3497-3531. (Pubitemid 34919207)
39. Mandal M, Lee M, Barrick JE, Weinberg Z, Emilsson GM, Ruzzo WL, Breaker RR. 2004. A glycine-dependent riboswitch that uses cooperative binding to control gene expression. Science 306: 275-279. (Pubitemid 39336872)
40. Martinez HM, Maizel JV, Shapiro B. 2008. RNA2D3D: A program for generating, viewing, and comparing 3-dimensional models of RNA. J Biomol Struct Dyn 25: 669-683. (Pubitemid 351694136)
41. Marti-Renom MA, Madhusudhan MS, Fiser A, Rost B, Sali A. 2002. Reliability of assessment of protein structure prediction methods. Structure 10: 435-440. (Pubitemid 34230630)
42. 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: 911-940. (Pubitemid 29248642)
43. Matthews B. 1975. Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim Biophys Acta 405: 442-451.
44. Metropolis N, Ulam S. 1949. The Monte Carlo method. J Am Stat Assoc 44: 335-341.
45. Michel F, Westhof E. 1990. Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J Mol Biol 216: 585-610. (Pubitemid 120037393)
46. Montange RK, Batey RT. 2006. Structure of the S-adenosylmethionine riboswitch regulatory mRNA element. Nature 441: 1172-1175. (Pubitemid 43990740)
47. Moult J. 2006. Rigorous performance evaluation in protein structure modelling and implications for computational biology. Philos Trans R Soc Lond B Biol Sci 361: 453-458. (Pubitemid 44870101)
48. Murray LJW, Arendall WB, Richardson DC, Richardson JS. 2003. RNA backbone is rotameric. Proc Natl Acad Sci 100: 13904-13909. (Pubitemid 37499164)
49. Parisien M, Major F. 2008. The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data. Nature 452: 51-55. (Pubitemid 351355097)
50. Parisien M, Cruz JA, Westhof E, Major F. 2009. New metrics for comparing and assessing discrepancies between RNA 3D structures and models. RNA 15: 1875-1885.
51. Qian B, Raman S, Das R, Bradley P, McCoy AJ, Read RJ, Baker D. 2007. High-resolution structure prediction and the crystallographic phase problem. Nature 450: 259-264. (Pubitemid 350100534)
52. Reuter JS, Mathews DH. 2010. RNAstructure: Software for RNA secondary structure prediction and analysis. BMC Bioinformatics 11: 129. doi: 10.1186/1471-2105-11-129.
53. Rother K, Rother M, Boniecki M, Puton T, Bujnicki JM. 2011a. RNA and protein 3D structure modeling: Similarities and differences. J Mol Model 17: 2325-2336.
54. Rother M, Rother K, Puton T, Bujnicki JM. 2011b. ModeRNA: A tool for comparative modeling of RNA 3D structure. Nucleic Acids Res 39: 4007-4022.
55. Rother K, Rother M, Boniecki M, Puton T, Tomala K, Lukasz P, Bujnicki JM. 2012. Template-based and template-free modeling of RNA 3D structure: Inspirations from protein structure modeling. In RNA 3D structure analysis and prediction (ed. NB Leontis, E Westhof). Springer-Verlag, Berlin.
56. Sarver M, Zirbel CL, Stombaugh J, Mokdad A, Leontis NB. 2008. FR3D: Finding local and composite recurrent structural motifs in RNA 3D structures. J Math Biol 56: 215-252. (Pubitemid 350172192)
57. Serra MJ, Axenson TJ, Turner DH. 1994. A model for the stabilities of RNA hairpins based on a study of the sequence dependence of stability for hairpins of six nucleotides. Biochemistry 33: 14289-14296. (Pubitemid 24382376)
58. Sherman Ma, Seth A, Delp SL. 2011. Simbody: Multibody dynamics for biomedical research. Procedia IUTAM 2: 241-261.
59. Sijenyi F, Saro P, Ouyang Z, Damm-Ganamet K, Wood M, Jiang J, SantaLucia J Jr. 2012. The RNA folding problems: Different levels of RNA structure prediction. In RNA 3D structure analysis and prediction (ed. NB Leontis, E Westhof). Springer-Verlag, Berlin.
60. Sripakdeevong P, Kladwang W, Das R. 2011. An enumerative stepwise ansatz enables atomic-accuracy RNA loop modeling. Proc Natl Acad Sci 108: 20573-20578.
61. Surles MC, Richardson JS, Richardson DC, Brooks FP. 1994. Sculpting proteins interactively: Continual energy minimization embedded in a graphical modeling system. Protein Sci 3: 198-210. (Pubitemid 24086353)
62. Tinoco I Jr, Bustamante C. 1999. How RNA folds. J Mol Biol 293: 271-281. (Pubitemid 29516169)
63. Tinoco I Jr, Borer PN, Dengler B, Levin MD, Uhlenbeck OC, Crothers DM, Bralla J. 1973. Improved estimation of secondary structure in ribonucleic acids. Nat New Biol 246: 40-41.
64. Woese CR, Magrum LJ, Gupta R, Siegel RB, Stahl DA, Kop J, Crawford N, Brosius J, Gutell R, Hogan JJ, et al. 1980. Secondary structure model for bacterial 16S ribosomal RNA: Phylogenetic, enzymatic and chemical evidence. Nucleic Acids Res 8: 2275-2293. (Pubitemid 10025762)
65. Word JM, Lovell SC, LaBean TH, Taylor HC, Zalis ME, Presley BK, Richardson JS, Richardson DC. 1999. Visualizing and quantifying molecular goodness-of-fit: Small-probe contact dots with explicit hydrogen atoms. J Mol Biol 285: 1711-1733. (Pubitemid 29060466)
66. Yang H, Jossinet F, Leontis N, Chen L, Westbrook J, Berman H, Westhof E. 2003. Tools for the automatic identification and classification of RNA base pairs. Nucleic Acids Res 31: 3450-3460. (Pubitemid 37442176)
67. Zemla A. 2003. LGA: A method for finding 3D similarities in protein structures. Nucleic Acids Res 31: 3370-3374. (Pubitemid 37442162)
68. Zhang Y, Skolnick J. 2004. Scoring function for automated assessment of protein structure template quality. Proteins 57: 702-710. (Pubitemid 39626992)
69. Zhao Q, Han Q, Kissinger CR, Hermann T, Thompson P. 2008. Structure of hepatitis C virus IRES subdomain IIa. Acta Crystallogr D Biol Crystallogr 64: 436-443. (Pubitemid 351507806)
70. Zuker M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406-3415. (Pubitemid 37442169)