Articles with public access mandates - Craig L.ZirbelLearn more
Available somewhere: 29
Frequency and isostericity of RNA base pairs
J Stombaugh, CL Zirbel, E Westhof, NB Leontis
Nucleic acids research 37 (7), 2294-2312, 2009
Mandates: US National Institutes of Health
The Nucleic Acid Database: new features and capabilities
B Coimbatore Narayanan, J Westbrook, S Ghosh, AI Petrov, B Sweeney, ...
Nucleic acids research 42 (D1), D114-D122, 2014
Mandates: US National Institutes of Health
Classification and energetics of the base-phosphate interactions in RNA
CL Zirbel, JE Šponer, J Šponer, J Stombaugh, NB Leontis
Nucleic acids research 37 (15), 4898-4918, 2009
Mandates: US National Institutes of Health
Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas
AI Petrov, CL Zirbel, NB Leontis
Rna 19 (10), 1327-1340, 2013
Mandates: US National Institutes of Health
Nonredundant 3D structure datasets for RNA knowledge extraction and benchmarking
NB Leontis, CL Zirbel
RNA 3D structure analysis and prediction, 281-298, 2012
Mandates: US National Institutes of Health
Comprehensive survey and geometric classification of base triples in RNA structures
AS Abu Almakarem, AI Petrov, J Stombaugh, CL Zirbel, NB Leontis
Nucleic Acids Research 40 (4), 1407-1423, 2012
Mandates: US National Institutes of Health
WebFR3D—a server for finding, aligning and analyzing recurrent RNA 3D motifs
AI Petrov, CL Zirbel, NB Leontis
Nucleic acids research 39 (suppl_2), W50-W55, 2011
Mandates: US National Institutes of Health
R3D Align: global pairwise alignment of RNA 3D structures using local superpositions
RR Rahrig, NB Leontis, CL Zirbel
Bioinformatics 26 (21), 2689-2697, 2010
Mandates: US National Institutes of Health
Identifying novel sequence variants of RNA 3D motifs
CL Zirbel, J Roll, BA Sweeney, AI Petrov, M Pirrung, NB Leontis
Nucleic acids research 43 (15), 7504-7520, 2015
Mandates: US National Institutes of Health
The RNA 3D Motif Atlas: Computational methods for extraction, organization and evaluation of RNA motifs
LG Parlea, BA Sweeney, M Hosseini-Asanjan, CL Zirbel, NB Leontis
Methods 103, 99-119, 2016
Mandates: US National Institutes of Health
Sharing and archiving nucleic acid structure mapping data
P Rocca-Serra, S Bellaousov, A Birmingham, C Chen, P Cordero, R Das, ...
Rna 17 (7), 1204-1212, 2011
Mandates: US National Institutes of Health, Howard Hughes Medical Institute
Isosteric and nonisosteric base pairs in RNA motifs: Molecular dynamics and bioinformatics study of the sarcin–ricin internal loop
M Havrila, K Réblová, CL Zirbel, NB Leontis, J Šponer
The journal of physical chemistry B 117 (46), 14302-14319, 2013
Mandates: US National Institutes of Health
RNA 3-dimensional structural motifs as a critical constraint of viroid RNA evolution
Y Wang, CL Zirbel, NB Leontis, B Ding
PLoS Pathogens 14 (2), e1006801, 2018
Mandates: US National Science Foundation
A three-dimensional RNA motif mediates directional trafficking of Potato spindle tuber viroid from epidermal to palisade mesophyll cells in Nicotiana benthamiana
J Wu, NB Leontis, CL Zirbel, DM Bisaro, B Ding
PLoS Pathogens 15 (10), e1008147, 2019
Mandates: US National Science Foundation, US Department of Agriculture
JAR3D Webserver: Scoring and aligning RNA loop sequences to known 3D motifs
J Roll, CL Zirbel, B Sweeney, AI Petrov, N Leontis
Nucleic acids research 44 (W1), W320-W327, 2016
Mandates: US National Institutes of Health
Noncanonical hydrogen bonding in nucleic acids. Benchmark evaluation of Key base–phosphate interactions in folded RNA molecules using quantum-chemical calculations and …
M Zgarbova, P Jurecka, P Banas, M Otyepka, JE Sponer, NB Leontis, ...
The Journal of Physical Chemistry A 115 (41), 11277-11292, 2011
Mandates: US National Institutes of Health
Functional analysis reveals G/U pairs critical for replication and trafficking of an infectious non-coding viroid RNA
J Wu, C Zhou, J Li, C Li, X Tao, NB Leontis, CL Zirbel, DM Bisaro, B Ding
Nucleic acids research 48 (6), 3134-3155, 2020
Mandates: US National Science Foundation, US National Institutes of Health, US …
RNA 3D modules in genome-wide predictions of RNA 2D structure
C Theis, CL Zirbel, CH Zu Siederdissen, C Anthon, IL Hofacker, H Nielsen, ...
PLoS One 10 (10), e0139900, 2015
Mandates: US National Institutes of Health, Austrian Science Fund, Innovation Fund Denmark
R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures
RR Rahrig, AI Petrov, NB Leontis, CL Zirbel
Nucleic acids research 41 (W1), W15-W21, 2013
Mandates: US National Institutes of Health
How to fold and protect mitochondrial ribosomal RNA with fewer guanines
M Hosseini, P Roy, M Sissler, CL Zirbel, E Westhof, N Leontis
Nucleic Acids Research 46 (20), 10946-10968, 2018
Mandates: US National Institutes of Health
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