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Neocles B. Leontis - Publications

1987- Chemistry Bowling Green State University, Bowling Green, OH, United States 
3D architecture of single-stranded DNA and RNA

81 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Parlea L, Sweeney BA, Zirbel CL, Leontis NB. The RNA 3D Motif Atlas: Computational Methods for Extraction, Organization and Evaluation of RNA Motifs. Methods (San Diego, Calif.). PMID 27125735 DOI: 10.1016/J.Ymeth.2016.04.025  1
2015 Zirbel CL, Roll J, Sweeney BA, Petrov AI, Pirrung M, Leontis NB. Identifying novel sequence variants of RNA 3D motifs. Nucleic Acids Research. 43: 7504-20. PMID 26130723 DOI: 10.1093/Nar/Gkv651  1
2015 Sweeney BA, Roy P, Leontis NB. An introduction to recurrent nucleotide interactions in RNA. Wiley Interdisciplinary Reviews. Rna. 6: 17-45. PMID 25664365 DOI: 10.1002/Wrna.1258  1
2015 Khisamutdinov EF, Shamaev AE, Karabaeva KE, Mereshchenko AS, Panov MS, Rabahalsulami, Boda PA, Leontis NB, Tarnovsky AN, Wilson RM. A pyrene dihydrodioxin with pyridinium "arms": A photochemically active DNA cleaving agent with unusual duplex stabilizing and electron trapping properties Journal of Photochemistry and Photobiology a: Chemistry. 307: 131-146. DOI: 10.1016/J.Jphotochem.2015.03.017  1
2014 Leontis NB, Westhof E. Chemistry. Self-assembled RNA nanostructures. Science (New York, N.Y.). 345: 732-3. PMID 25124412 DOI: 10.1126/Science.1257989  1
2014 Coimbatore Narayanan B, Westbrook J, Ghosh S, Petrov AI, Sweeney B, Zirbel CL, Leontis NB, Berman HM. The Nucleic Acid Database: new features and capabilities. Nucleic Acids Research. 42: D114-22. PMID 24185695 DOI: 10.1093/Nar/Gkt980  1
2013 Havrila M, Réblová K, Zirbel CL, Leontis NB, Šponer J. Isosteric and nonisosteric base pairs in RNA motifs: molecular dynamics and bioinformatics study of the sarcin-ricin internal loop. The Journal of Physical Chemistry. B. 117: 14302-19. PMID 24144333 DOI: 10.1021/Jp408530W  1
2013 Qiu M, Khisamutdinov E, Zhao Z, Pan C, Choi JW, Leontis NB, Guo P. RNA nanotechnology for computer design and in vivo computation. Philosophical Transactions. Series a, Mathematical, Physical, and Engineering Sciences. 371: 20120310. PMID 24000362 DOI: 10.1098/Rsta.2012.0310  1
2013 Petrov AI, Zirbel CL, Leontis NB. Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas. Rna (New York, N.Y.). 19: 1327-40. PMID 23970545 DOI: 10.1261/Rna.039438.113  1
2013 Rahrig RR, Petrov AI, Leontis NB, Zirbel CL. R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures. Nucleic Acids Research. 41: W15-21. PMID 23716643 DOI: 10.1093/Nar/Gkt417  1
2013 Petrov AI, Sweeney BA, Leontis NB. Analyzing, searching, and annotating recurrent RNA three-dimensional motifs Rna Structure and Folding: Biophysical Techniques and Prediction Methods. 363-398. DOI: 10.1515/9783110284959.363  1
2012 Cruz JA, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cao S, Das R, Ding F, Dokholyan NV, Flores SC, Huang L, Lavender CA, Lisi V, Major F, Mikolajczak K, ... ... Leontis NB, et al. RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction. Rna (New York, N.Y.). 18: 610-25. PMID 22361291 DOI: 10.1261/Rna.031054.111  1
2012 Abu Almakarem AS, Petrov AI, Stombaugh J, Zirbel CL, Leontis NB. Comprehensive survey and geometric classification of base triples in RNA structures. Nucleic Acids Research. 40: 1407-23. PMID 22053086 DOI: 10.1093/Nar/Gkr810  1
2011 Zgarbová M, Jurečka P, Banáš P, Otyepka M, Sponer JE, Leontis NB, Zirbel CL, Sponer J. Noncanonical hydrogen bonding in nucleic acids. Benchmark evaluation of key base-phosphate interactions in folded RNA molecules using quantum-chemical calculations and molecular dynamics simulations. The Journal of Physical Chemistry. A. 115: 11277-92. PMID 21910417 DOI: 10.1021/Jp204820B  1
2011 Birmingham A, Clemente JC, Desai N, Gilbert J, Gonzalez A, Kyrpides N, Meyer F, Nawrocki E, Sterk P, Stombaugh J, Weinberg Z, Wendel D, Leontis NB, Zirbel C, Knight R, et al. Meeting report of the RNA Ontology Consortium January 8-9, 2011. Standards in Genomic Sciences. 4: 252-6. PMID 21677862 DOI: 10.4056/Sigs.1724282  1
2011 Rocca-Serra P, Bellaousov S, Birmingham A, Chen C, Cordero P, Das R, Davis-Neulander L, Duncan CD, Halvorsen M, Knight R, Leontis NB, Mathews DH, Ritz J, Stombaugh J, Weeks KM, et al. Sharing and archiving nucleic acid structure mapping data. Rna (New York, N.Y.). 17: 1204-12. PMID 21610212 DOI: 10.1261/Rna.2753211  1
2011 Petrov AI, Zirbel CL, Leontis NB. WebFR3D--a server for finding, aligning and analyzing recurrent RNA 3D motifs. Nucleic Acids Research. 39: W50-5. PMID 21515634 DOI: 10.1093/Nar/Gkr249  1
2011 Takeda R, Petrov AI, Leontis NB, Ding B. A three-dimensional RNA motif in Potato spindle tuber viroid mediates trafficking from palisade mesophyll to spongy mesophyll in Nicotiana benthamiana. The Plant Cell. 23: 258-72. PMID 21258006 DOI: 10.1105/Tpc.110.081414  1
2011 Novikova IV, Hassan BH, Mirzoyan MG, Leontis NB. Engineering cooperative tecto-RNA complexes having programmable stoichiometries. Nucleic Acids Research. 39: 2903-17. PMID 21138969 DOI: 10.1093/Nar/Gkq1231  1
2011 Hoehndorf R, Batchelor C, Bittner T, Dumontier M, Eilbeck K, Knight R, Mungall CJ, Richardson JS, Stombaugh J, Westhof E, Zirbel CL, Leontis NB. The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data Applied Ontology. 6: 53-89. DOI: 10.1038/Npre.2009.3561.1  1
2010 Å poner J, Å poner JE, Petrov AI, Leontis NB. Quantum chemical studies of nucleic acids: can we construct a bridge to the RNA structural biology and bioinformatics communities? The Journal of Physical Chemistry. B. 114: 15723-41. PMID 21049899 DOI: 10.1021/Jp104361M  1
2010 Rahrig RR, Leontis NB, Zirbel CL. R3D Align: global pairwise alignment of RNA 3D structures using local superpositions. Bioinformatics (Oxford, England). 26: 2689-97. PMID 20929913 DOI: 10.1093/Bioinformatics/Btq506  1
2010 Besseová I, Réblová K, Leontis NB, Sponer J. Molecular dynamics simulations suggest that RNA three-way junctions can act as flexible RNA structural elements in the ribosome. Nucleic Acids Research. 38: 6247-64. PMID 20507916 DOI: 10.1093/Nar/Gkq414  1
2009 Brown JW, Birmingham A, Griffiths PE, Jossinet F, Kachouri-Lafond R, Knight R, Lang BF, Leontis N, Steger G, Stombaugh J, Westhof E. The RNA structure alignment ontology. Rna (New York, N.Y.). 15: 1623-31. PMID 19622678 DOI: 10.1261/rna.1601409  1
2009 Zirbel CL, Sponer JE, Sponer J, Stombaugh J, Leontis NB. Classification and energetics of the base-phosphate interactions in RNA. Nucleic Acids Research. 37: 4898-918. PMID 19528080 DOI: 10.1093/Nar/Gkp468  1
2009 Stombaugh J, Zirbel CL, Westhof E, Leontis NB. Frequency and isostericity of RNA base pairs. Nucleic Acids Research. 37: 2294-312. PMID 19240142 DOI: 10.1093/Nar/Gkp011  1
2009 Petrov AI, Stombaugh J, Zirbel CL, Leontis NB. Understanding sequence variability of RNA motifs using geometric search and IsoDiscrepancy matrices Occbio'09: 2009 Ohio Collaborative Conference On Bioinformatics. 45-50. DOI: 10.1109/OCCBIO.2009.15  1
2008 Xin Y, Laing C, Leontis NB, Schlick T. Annotation of tertiary interactions in RNA structures reveals variations and correlations. Rna (New York, N.Y.). 14: 2465-77. PMID 18957492 DOI: 10.1261/Rna.1249208  1
2008 Afonin KA, Danilov EO, Novikova IV, Leontis NB. TokenRNA: a new type of sequence-specific, label-free fluorescent biosensor for folded RNA molecules. Chembiochem : a European Journal of Chemical Biology. 9: 1902-5. PMID 18655086 DOI: 10.1002/Cbic.200800183  1
2008 Afonin KA, Cieply DJ, Leontis NB. Specific RNA self-assembly with minimal paranemic motifs. Journal of the American Chemical Society. 130: 93-102. PMID 18072767 DOI: 10.1021/Ja071516M  1
2008 Sarver M, Zirbel CL, Stombaugh J, Mokdad A, Leontis NB. FR3D: Finding local and composite recurrent structural motifs in RNA 3D structures Journal of Mathematical Biology. 56: 215-252. PMID 17694311 DOI: 10.1007/S00285-007-0110-X  1
2007 Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, et al. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nature Biotechnology. 25: 1251-5. PMID 17989687 DOI: 10.1038/Nbt1346  1
2006 Afonin KA, Leontis NB. Generating new specific RNA interaction interfaces using C-loops. Journal of the American Chemical Society. 128: 16131-7. PMID 17165766 DOI: 10.1021/Ja064289H  1
2006 Zhong X, Leontis N, Qian S, Itaya A, Qi Y, Boris-Lawrie K, Ding B. Tertiary structural and functional analyses of a viroid RNA motif by isostericity matrix and mutagenesis reveal its essential role in replication. Journal of Virology. 80: 8566-81. PMID 16912306 DOI: 10.1128/Jvi.00837-06  1
2006 Mokdad A, Leontis NB. Ribostral: an RNA 3D alignment analyzer and viewer based on basepair isostericities. Bioinformatics (Oxford, England). 22: 2168-70. PMID 16820430 DOI: 10.1093/Bioinformatics/Btl360  1
2006 Leontis NB, Lescoute A, Westhof E. The building blocks and motifs of RNA architecture. Current Opinion in Structural Biology. 16: 279-87. PMID 16713707 DOI: 10.1016/J.Sbi.2006.05.009  1
2006 Nasalean L, Baudrey S, Leontis NB, Jaeger L. Controlling RNA self-assembly to form filaments. Nucleic Acids Research. 34: 1381-92. PMID 16522648 DOI: 10.1093/Nar/Gkl008  1
2006 Mokdad A, Krasovska MV, Sponer J, Leontis NB. Structural and evolutionary classification of G/U wobble basepairs in the ribosome. Nucleic Acids Research. 34: 1326-41. PMID 16522645 DOI: 10.1093/Nar/Gkl025  1
2006 Leontis NB, Altman RB, Berman HM, Brenner SE, Brown JW, Engelke DR, Harvey SC, Holbrook SR, Jossinet F, Lewis SE, Major F, Mathews DH, Richardson JS, Williamson JR, Westhof E. The RNA Ontology Consortium: an open invitation to the RNA community. Rna (New York, N.Y.). 12: 533-41. PMID 16484377 DOI: 10.1261/Rna.2343206  1
2005 Lescoute A, Leontis NB, Massire C, Westhof E. Recurrent structural RNA motifs, Isostericity Matrices and sequence alignments. Nucleic Acids Research. 33: 2395-409. PMID 15860776 DOI: 10.1093/Nar/Gki535  1
2005 Rázga F, Koca J, Sponer J, Leontis NB. Hinge-like motions in RNA kink-turns: the role of the second a-minor motif and nominally unpaired bases. Biophysical Journal. 88: 3466-85. PMID 15722438 DOI: 10.1529/Biophysj.104.054916  1
2004 Réblová K, Spacková N, Koca J, Leontis NB, Sponer J. Long-residency hydration, cation binding, and dynamics of loop E/helix IV rRNA-L25 protein complex. Biophysical Journal. 87: 3397-412. PMID 15339800 DOI: 10.1529/Biophysj.104.047126  1
2004 Rázga F, Spackova N, Réblova K, Koca J, Leontis NB, Sponer J. Ribosomal RNA kink-turn motif--a flexible molecular hinge. Journal of Biomolecular Structure & Dynamics. 22: 183-94. PMID 15317479 DOI: 10.1080/07391102.2004.10506994  1
2003 Sponer J, Mokdad A, Sponer JE, Spacková N, Leszczynski J, Leontis NB. Unique tertiary and neighbor interactions determine conservation patterns of Cis Watson-Crick A/G base-pairs. Journal of Molecular Biology. 330: 967-78. PMID 12860120 DOI: 10.1016/S0022-2836(03)00667-3  1
2003 Leontis NB, Westhof E. Analysis of RNA motifs. Current Opinion in Structural Biology. 13: 300-8. PMID 12831880 DOI: 10.1016/S0959-440X(03)00076-9  1
2003 Réblová K, Spacková N, Stefl R, Csaszar K, Koca J, Leontis NB, Sponer J. Non-Watson-Crick basepairing and hydration in RNA motifs: molecular dynamics of 5S rRNA loop E. Biophysical Journal. 84: 3564-82. PMID 12770867 DOI: 10.1016/S0006-3495(03)75089-9  1
2002 Leontis NB, Westhof E. The annotation of RNA motifs. Comparative and Functional Genomics. 3: 518-24. PMID 18629252 DOI: 10.1002/Cfg.213  1
2002 Leontis NB, Stombaugh J, Westhof E. Motif prediction in ribosomal RNAs: Lessons and prospects for automated motif prediction in homologous RNA molecules Biochimie. 84: 961-973. PMID 12458088 DOI: 10.1016/S0300-9084(02)01463-3  1
2002 Leontis NB, Stombaugh J, Westhof E. The non-Watson-Crick base pairs and their associated isostericity matrices. Nucleic Acids Research. 30: 3497-531. PMID 12177293 DOI: 10.1093/Nar/Gkf481  1
2002 Waugh A, Gendron P, Altman R, Brown JW, Case D, Gautheret D, Harvey SC, Leontis N, Westbrook J, Westhof E, Zuker M, Major F. RNAML: a standard syntax for exchanging RNA information. Rna (New York, N.Y.). 8: 707-17. PMID 12088144 DOI: 10.1017/S1355838202028017  1
2002 Myshkin E, Leontis NB, Bullerjahn GS. Computational simulation of the docking of Prochlorothrix hollandica plastocyanin to potosystem I: modeling the electron transfer complex. Biophysical Journal. 82: 3305-13. PMID 12023253 DOI: 10.1016/S0006-3495(02)75671-3  1
2001 Csaszar K, Špačková N, Štefl R, Šponer J, Leontis NB. Molecular dynamics of the frame-shifting pseudoknot from beet western yellows virus: The role of non-Watson-Crick base-pairing, ordered hydration, cation binding and base mutations on stability and unfolding Journal of Molecular Biology. 313: 1073-1091. PMID 11700064 DOI: 10.1006/Jmbi.2001.5100  1
2001 Leontis NB, Westhof E. Geometric nomenclature and classification of RNA base pairs Rna. 7: 499-512. PMID 11345429 DOI: 10.1017/S1355838201002515  1
2001 Jaeger L, Westhof E, Leontis NB. TectoRNA: Modular assembly units for the construction of RNA nano-objects Nucleic Acids Research. 29: 455-463. PMID 11139616 DOI: 10.1093/Nar/29.2.455  1
2000 Thiviyanathan V, Guliaev AB, Leontis NB, Gorenstein DG. Solution conformation of a bulged adenosine base in an RNA duplex by relaxation matrix refinement Journal of Molecular Biology. 300: 1143-1154. PMID 10903860 DOI: 10.1006/Jmbi.2000.3931  1
2000 Aoudia M, Guliaev AB, Leontis NB, Rodgers MAJ. Self-assembled complexes of oligopeptides and metalloporphyrins: Measurements of the reorganization and electronic interaction energies for photoinduced electron-transfer reactions Biophysical Chemistry. 83: 121-140. PMID 10672418 DOI: 10.1016/S0301-4622(99)00128-3  1
2000 Jaeger L, Leontis NB. Tecto-RNA: One-dimensional self-assembly through tertiary interactions Angewandte Chemie - International Edition. 39: 2521-2524. DOI: 10.1002/1521-3773(20000717)39:14<2521::Aid-Anie2521>3.0.Co;2-P  1
1999 Guliaev AB, Leontis NB. Cationic 5,10,15,20-tetrakis (N-methylpyridinium-4-yl) porphyrin fully intercalates at 5'-CG-3' steps of duplex DNA in solution Biochemistry. 38: 15425-15437. PMID 10569925 DOI: 10.1021/Bi9913808  1
1999 Thiviyanathan V, Luxon BA, Leontis NB, Illangasekare N, Donne DG, Gorenstein DG. Hybrid-hybrid matrix structural refinement of a DNA three-way junction from 3D NOESY-NOESY Journal of Biomolecular Nmr. 14: 209-221. PMID 10481274 DOI: 10.1023/A:1008330011425  1
1998 Leontis NB, Westhof E. Conserved geometrical base-pairing patterns in RNA Quarterly Reviews of Biophysics. 31: 399-455. PMID 10709244 DOI: 10.1017/S0033583599003479  1
1998 Leontis NB, Westhof E. A common motif organizes the structure of multi-helix loops in 16 S and 23 S ribosomal RNAs Journal of Molecular Biology. 283: 571-583. PMID 9784367 DOI: 10.1006/Jmbi.1998.2106  1
1998 Leontis NB, Westhof E. The 5S rRNA loop E: Chemical probing and phylogenetic data versus crystal structure Rna. 4: 1134-1153. PMID 9740131 DOI: 10.1017/S1355838298980566  1
1998 Woodson SA, Leontis NB. Structure and dynamics of ribosomal RNA. Current Opinion in Structural Biology. 8: 294-300. PMID 9666324 DOI: 10.1016/S0959-440X(98)80061-4  1
1998 Leontis NB, SantaLucia J. Overview Acs Symposium Series. 682: 1-16.  1
1998 Thiviyanthan V, Illangasekare N, Gozansky E, Zhu F, Leontis NB, Luxon BA, Gorenstein DG. Three-Dimensional NOESY-NOESY Hybrid-Hybrid Matrix Refinement of a DNA Three-Way Junction Acs Symposium Series. 682: 167-180.  1
1995 Leontis NB, Piotto ME, Hills MT, Malhotra A, Ouporov IV, Nussbaum JM, Gorenstein DG. Structural studies of DNA three-way junctions. Methods in Enzymology. 261: 183-207. PMID 8569495 DOI: 10.1016/S0076-6879(95)61010-3  1
1995 Ouporov IV, Leontis NB. Refinement of the solution structure of a branched DNA three-way junction Biophysical Journal. 68: 266-274. PMID 7711250 DOI: 10.1016/S0006-3495(95)80183-9  1
1995 Leontis NB, Hills MT, Piotto M, Ouporov IV, Malhotra A, Gorenstein DG. Helical stacking in DNA three-way junctions containing two unpaired pyrimidines: proton NMR studies. Biophysical Journal. 68: 251-65. PMID 7711249 DOI: 10.1016/S0006-3495(95)80182-7  1
1995 Kadrmas JL, Ravin AJ, Leontis NB. Relative stabilities of DNA three-way, four-way and five-way junctions (multi-helix junction loops): Unpaired nucleotides can be stabilizing or destabilizing Nucleic Acids Research. 23: 2212-2222. PMID 7610050 DOI: 10.1093/Nar/23.12.2212  1
1994 Ladbury JE, Sturtevant JM, Leontis NB. The thermodynamics of formation of a three-strand, DNA three-way junction complex. Biochemistry. 33: 6828-33. PMID 8204617 DOI: 10.1021/Bi00188A011  1
1994 Nussbaum JM, Newport ME, Mackie M, Leontis NB. Structure-specific binding and photosensitized cleavage of branched DNA three-way junction complexes by cationic porphyrins. Photochemistry and Photobiology. 59: 515-28. PMID 8041806 DOI: 10.1111/J.1751-1097.1994.Tb02977.X  1
1993 Leontis NB, Hills MT, Piotto M, Malhotra A, Nussbaum J, Gorenstein DG. A model for the solution structure of a branched, three-strand DNA complex. Journal of Biomolecular Structure & Dynamics. 11: 215-23. PMID 8286052 DOI: 10.1080/07391102.1993.10508722  1
1991 Leontis NB, Kwok W, Newman JS. Stability and structure of three-way DNA junctions containing unpaired nucleotides Nucleic Acids Research. 19: 759-766. PMID 2017361 DOI: 10.1093/Nar/19.4.759  1
1990 Zhou JS, Granada ESV, Leontis NB, Rodgers MAJ. Photoinduced electron transfer in self-associated complexes of several uroporphyrins and cytochrome c Journal of the American Chemical Society. 112: 5074-5080. DOI: 10.1021/Ja00169A012  1
1988 Moore PB, Abo S, Freeborn B, Gewirth DT, Leontis NB, Sun G. [10] Preparation of 5S RNA-related materials for nuclear magnetic resonance and crystallography studies Methods in Enzymology. 164: 158-174. PMID 3071660 DOI: 10.1016/S0076-6879(88)64041-9  1
1987 Gewirth DT, Abo SR, Leontis NB, Moore PB. Secondary structure of 5S RNA: NMR experiments on RNA molecules partially labeled with nitrogen-15 Biochemistry. 26: 5213-5220. PMID 2444255 DOI: 10.1021/Bi00390A047  1
1986 Leontis NB, Ghosh P, Moore PB. Effect of magnesium ion on the structure of the 5S RNA from Escherichia coli. An imino proton magnetic resonance study of the helix I, IV, and v regions of the molecule Biochemistry. 25: 7386-7392. PMID 3542026 DOI: 10.1021/Bi00371A021  1
1986 Leontis NB, Moore PB. Imino proton exchange in the 5S RNA of Escherichia coli and its complex with protein L25 at 490 MHz Biochemistry. 25: 5736-5744. PMID 3535886 DOI: 10.1021/Bi00367A058  1
1986 Leontis NB, Moore PB. NMR evidence for dynamic secondary structure in helices II and III of the 5S RNA of Escherichia coli Biochemistry. 25: 3916-3925. PMID 2427108 DOI: 10.1021/Bi00361A027  1
1984 Leontis NB, Moore PB. A small angle x-ray scattering study of a fragment derived from E. coli 5S RNA Nucleic Acids Research. 12: 2193-2203. PMID 6366745 DOI: 10.1093/Nar/12.4.2193  1
1983 Moore PB, Kime MJ, Leontis NB, Abdel-Meguid SS. Physical studies on a nucleoprotein from the ribosome of e. Coli Journal of Biomolecular Structure and Dynamics. 1: 383-393. PMID 6401116 DOI: 10.1080/07391102.1983.10507449  1
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