-
1
-
-
79953052076
-
Structural basis of cooperative ligand binding by the glycine riboswitch
-
E.B. Butler, Y. Xiong, J. Wang, and S.A. Strobel Structural basis of cooperative ligand binding by the glycine riboswitch Chemistry & Biology 18 3 2011 293 298 10.1016/j.chembiol.2011.01.013
-
(2011)
Chemistry & Biology
, vol.18
, Issue.3
, pp. 293-298
-
-
Butler, E.B.1
Xiong, Y.2
Wang, J.3
Strobel, S.A.4
-
2
-
-
84908130641
-
MOHCA-seq: RNA 3D models from single multiplexed proximity-mapping experiments
-
C. Cheng, F.-C. Chou, W. Kladwang, S. Tian, P. Cordero, and R. Das MOHCA-seq: RNA 3D models from single multiplexed proximity-mapping experiments bioRxiv 2014 10.1101/004556
-
(2014)
BioRxiv
-
-
Cheng, C.1
Chou, F.-C.2
Kladwang, W.3
Tian, S.4
Cordero, P.5
Das, R.6
-
3
-
-
84908586687
-
Blind predictions of DNA and RNA tweezers experiments with force and torque
-
F.C. Chou, J. Lipfert, and R. Das Blind predictions of DNA and RNA tweezers experiments with force and torque PLoS Computational Biology 10 8 2014 e1003756 10.1371/journal.pcbi.1003756
-
(2014)
PLoS Computational Biology
, vol.10
, Issue.8
, pp. e1003756
-
-
Chou, F.C.1
Lipfert, J.2
Das, R.3
-
4
-
-
84871957573
-
Correcting pervasive errors in RNA crystallography through enumerative structure prediction
-
F.C. Chou, P. Sripakdeevong, S.M. Dibrov, T. Hermann, and R. Das Correcting pervasive errors in RNA crystallography through enumerative structure prediction Nature Methods 10 1 2013 74 76 10.1038/nmeth.2262
-
(2013)
Nature Methods
, vol.10
, Issue.1
, pp. 74-76
-
-
Chou, F.C.1
Sripakdeevong, P.2
Dibrov, S.M.3
Hermann, T.4
Das, R.5
-
5
-
-
84866060803
-
Quantitative dimethyl sulfate mapping for automated RNA secondary structure inference
-
P. Cordero, W. Kladwang, C.C. VanLang, and R. Das Quantitative dimethyl sulfate mapping for automated RNA secondary structure inference Biochemistry 51 36 2012 7037 7039 10.1021/bi3008802
-
(2012)
Biochemistry
, vol.51
, Issue.36
, pp. 7037-7039
-
-
Cordero, P.1
Kladwang, W.2
Vanlang, C.C.3
Das, R.4
-
6
-
-
84934441351
-
The mutate-and-map protocol for inferring base pairs in structured RNA
-
P. Cordero, W. Kladwang, C.C. VanLang, and R. Das The mutate-and-map protocol for inferring base pairs in structured RNA Methods in Molecular Biology 1086 2014 53 77 10.1007/978-1-62703-667-2-4
-
(2014)
Methods in Molecular Biology
, vol.1086
, pp. 53-77
-
-
Cordero, P.1
Kladwang, W.2
Vanlang, C.C.3
Das, R.4
-
7
-
-
84869472916
-
An RNA mapping database for curating RNA structure mapping experiments
-
P. Cordero, J.B. Lucks, and R. Das An RNA mapping database for curating RNA structure mapping experiments Bioinformatics 28 22 2012 3006 3008 10.1093/bioinformatics/bts554
-
(2012)
Bioinformatics
, vol.28
, Issue.22
, pp. 3006-3008
-
-
Cordero, P.1
Lucks, J.B.2
Das, R.3
-
8
-
-
84863338065
-
RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction
-
J.A. Cruz, M.F. Blanchet, M. Boniecki, J.M. Bujnicki, S.J. Chen, and S. Cao RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction RNA 18 4 2012 610 625 10.1261/rna.031054.111
-
(2012)
RNA
, vol.18
, Issue.4
, pp. 610-625
-
-
Cruz, J.A.1
Blanchet, M.F.2
Boniecki, M.3
Bujnicki, J.M.4
Chen, S.J.5
Cao, S.6
-
10
-
-
77951643739
-
Atomic accuracy in predicting and designing noncanonical RNA structure
-
R. Das, J. Karanicolas, and D. Baker Atomic accuracy in predicting and designing noncanonical RNA structure Nature Methods 7 4 2010 291 294 10.1038/nmeth.1433
-
(2010)
Nature Methods
, vol.7
, Issue.4
, pp. 291-294
-
-
Das, R.1
Karanicolas, J.2
Baker, D.3
-
11
-
-
41949089022
-
Structural inference of native and partially folded RNA by high-throughput contact mapping
-
R. Das, M. Kudaravalli, M. Jonikas, A. Laederach, R. Fong, and J.P. Schwans Structural inference of native and partially folded RNA by high-throughput contact mapping Proceedings of the National Academy of Sciences of the United States of America 105 11 2008 4144 4149 10.1073/pnas.0709032105
-
(2008)
Proceedings of the National Academy of Sciences of the United States of America
, vol.105
, Issue.11
, pp. 4144-4149
-
-
Das, R.1
Kudaravalli, M.2
Jonikas, M.3
Laederach, A.4
Fong, R.5
Schwans, J.P.6
-
12
-
-
75449112058
-
Molecular dynamics and quantum mechanics of RNA: Conformational and chemical change we can believe in
-
M.A. Ditzler, M. Otyepka, J. Sponer, and N.G. Walter Molecular dynamics and quantum mechanics of RNA: Conformational and chemical change we can believe in Accounts of Chemical Research 43 1 2010 40 47 10.1021/ar900093g
-
(2010)
Accounts of Chemical Research
, vol.43
, Issue.1
, pp. 40-47
-
-
Ditzler, M.A.1
Otyepka, M.2
Sponer, J.3
Walter, N.G.4
-
13
-
-
78650424317
-
Identification of a tertiary interaction important for cooperative ligand binding by the glycine riboswitch
-
T.V. Erion, and S.A. Strobel Identification of a tertiary interaction important for cooperative ligand binding by the glycine riboswitch RNA 17 1 2011 74 84 10.1261/rna.2271511
-
(2011)
RNA
, vol.17
, Issue.1
, pp. 74-84
-
-
Erion, T.V.1
Strobel, S.A.2
-
14
-
-
84875865461
-
Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots
-
C.E. Hajdin, S. Bellaousov, W. Huggins, C.W. Leonard, D.H. Mathews, and K.M. Weeks Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots Proceedings of the National Academy of Sciences of the United States of America 110 14 2013 5498 5503 10.1073/pnas.1219988110
-
(2013)
Proceedings of the National Academy of Sciences of the United States of America
, vol.110
, Issue.14
, pp. 5498-5503
-
-
Hajdin, C.E.1
Bellaousov, S.2
Huggins, W.3
Leonard, C.W.4
Mathews, D.H.5
Weeks, K.M.6
-
15
-
-
84883562900
-
HiTRACE-Web: An online tool for robust analysis of high-throughput capillary electrophoresis
-
H. Kim, P. Cordero, R. Das, and S. Yoon HiTRACE-Web: An online tool for robust analysis of high-throughput capillary electrophoresis Nucleic Acids Research 41 Web Server issue 2013 W492 W498 10.1093/nar/gkt501
-
(2013)
Nucleic Acids Research
, vol.41
, Issue.WEB SERVER ISSUE
, pp. W492-W498
-
-
Kim, H.1
Cordero, P.2
Das, R.3
Yoon, S.4
-
16
-
-
84856246110
-
Automated RNA structure prediction uncovers a kink-turn linker in double glycine riboswitches
-
W. Kladwang, F.C. Chou, and R. Das Automated RNA structure prediction uncovers a kink-turn linker in double glycine riboswitches Journal of the American Chemical Society 134 3 2012 1404 1407 10.1021/ja2093508
-
(2012)
Journal of the American Chemical Society
, vol.134
, Issue.3
, pp. 1404-1407
-
-
Kladwang, W.1
Chou, F.C.2
Das, R.3
-
17
-
-
84901029243
-
Standardization of RNA chemical mapping experiments
-
W. Kladwang, T.H. Mann, A. Becka, S. Tian, H. Kim, and S. Yoon Standardization of RNA chemical mapping experiments Biochemistry 53 19 2014 3063 3065 10.1021/bi5003426
-
(2014)
Biochemistry
, vol.53
, Issue.19
, pp. 3063-3065
-
-
Kladwang, W.1
Mann, T.H.2
Becka, A.3
Tian, S.4
Kim, H.5
Yoon, S.6
-
18
-
-
82055176702
-
A two-dimensional mutate-and-map strategy for non-coding RNA structure
-
W. Kladwang, C.C. VanLang, P. Cordero, and R. Das A two-dimensional mutate-and-map strategy for non-coding RNA structure Nature Chemistry 3 12 2011 954 962 10.1038/nchem.1176
-
(2011)
Nature Chemistry
, vol.3
, Issue.12
, pp. 954-962
-
-
Kladwang, W.1
Vanlang, C.C.2
Cordero, P.3
Das, R.4
-
19
-
-
78650905964
-
ROSETTA3: An object-oriented software suite for the simulation and design of macromolecules
-
A. Leaver-Fay, M. Tyka, S.M. Lewis, O.F. Lange, J. Thompson, and R. Jacak ROSETTA3: An object-oriented software suite for the simulation and design of macromolecules Methods in Enzymology 487 2011 545 574 10.1016/B978-0-12-381270-4.00019-6
-
(2011)
Methods in Enzymology
, vol.487
, pp. 545-574
-
-
Leaver-Fay, A.1
Tyka, M.2
Lewis, S.M.3
Lange, O.F.4
Thompson, J.5
Jacak, R.6
-
20
-
-
84893831061
-
RNA design rules from a massive open laboratory
-
J. Lee, W. Kladwang, M. Lee, D. Cantu, M. Azizyan, and H. Kim RNA design rules from a massive open laboratory Proceedings of the National Academy of Sciences of the United States of America 111 6 2014 2122 2127 10.1073/pnas.1313039111
-
(2014)
Proceedings of the National Academy of Sciences of the United States of America
, vol.111
, Issue.6
, pp. 2122-2127
-
-
Lee, J.1
Kladwang, W.2
Lee, M.3
Cantu, D.4
Azizyan, M.5
Kim, H.6
-
21
-
-
84878087999
-
Serverification of molecular modeling applications: The Rosetta online server that includes everyone (ROSIE)
-
S. Lyskov, F.C. Chou, S.O. Conchuir, B.S. Der, K. Drew, and D. Kuroda Serverification of molecular modeling applications: The Rosetta online server that includes everyone (ROSIE) PLoS One 8 5 2013 e63906 10.1371/journal.pone.0063906
-
(2013)
PLoS One
, vol.8
, Issue.5
, pp. e63906
-
-
Lyskov, S.1
Chou, F.C.2
Conchuir, S.O.3
Der, B.S.4
Drew, K.5
Kuroda, D.6
-
22
-
-
84884679567
-
Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas
-
A.I. Petrov, C.L. Zirbel, and N.B. Leontis Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas RNA 19 10 2013 1327 1340 10.1261/rna.039438.113
-
(2013)
RNA
, vol.19
, Issue.10
, pp. 1327-1340
-
-
Petrov, A.I.1
Zirbel, C.L.2
Leontis, N.B.3
-
23
-
-
84883579142
-
R3D align web server for global nucleotide to nucleotide alignments of RNA 3D structures
-
R.R. Rahrig, A.I. Petrov, N.B. Leontis, and C.L. Zirbel R3D align web server for global nucleotide to nucleotide alignments of RNA 3D structures Nucleic Acids Research 41 Web Server issue 2013 W15 W21 10.1093/nar/gkt417
-
(2013)
Nucleic Acids Research
, vol.41
, Issue.WEB SERVER ISSUE
, pp. W15-W21
-
-
Rahrig, R.R.1
Petrov, A.I.2
Leontis, N.B.3
Zirbel, C.L.4
-
24
-
-
77949447172
-
RNAstructure: Software for RNA secondary structure prediction and analysis
-
J.S. Reuter, and D.H. Mathews RNAstructure: Software for RNA secondary structure prediction and analysis BMC Bioinformatics 11 2010 129 10.1186/1471-2105-11-129
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 129
-
-
Reuter, J.S.1
Mathews, D.H.2
-
25
-
-
36448954303
-
FR3D: Finding local and composite recurrent structural motifs in RNA 3D structures
-
M. Sarver, C.L. Zirbel, J. Stombaugh, A. Mokdad, and N.B. Leontis FR3D: Finding local and composite recurrent structural motifs in RNA 3D structures Journal of Mathematical Biology 56 1-2 2008 215 252 10.1007/s00285-007-0110-x
-
(2008)
Journal of Mathematical Biology
, vol.56
, Issue.12
, pp. 215-252
-
-
Sarver, M.1
Zirbel, C.L.2
Stombaugh, J.3
Mokdad, A.4
Leontis, N.B.5
-
27
-
-
84934435385
-
Massively parallel RNA chemical mapping with a reduced bias MAP-seq protocol
-
M.G. Seetin, W. Kladwang, J.P. Bida, and R. Das Massively parallel RNA chemical mapping with a reduced bias MAP-seq protocol Methods in Molecular Biology 1086 2014 95 117 10.1007/978-1-62703-667-2-6
-
(2014)
Methods in Molecular Biology
, vol.1086
, pp. 95-117
-
-
Seetin, M.G.1
Kladwang, W.2
Bida, J.P.3
Das, R.4
-
29
-
-
84888623229
-
Why can't we predict RNA structure at atomic resolution?
-
N.B. Leontis, E. Westhof, Springer Heidelberg, New York 400 p
-
P. Sripakdeevong, K. Beauchamp, and R. Das Why can't we predict RNA structure at atomic resolution? N.B. Leontis, E. Westhof, RNA 3D structure analysis and prediction 2012 Springer Heidelberg, New York 400 p
-
(2012)
RNA 3D Structure Analysis and Prediction
-
-
Sripakdeevong, P.1
Beauchamp, K.2
Das, R.3
-
30
-
-
84897954661
-
Structure determination of noncanonical RNA motifs guided by (1)H NMR chemical shifts
-
P. Sripakdeevong, M. Cevec, A.T. Chang, M.C. Erat, M. Ziegeler, and Q. Zhao Structure determination of noncanonical RNA motifs guided by (1)H NMR chemical shifts Nature Methods 11 4 2014 413 416 10.1038/nmeth.2876
-
(2014)
Nature Methods
, vol.11
, Issue.4
, pp. 413-416
-
-
Sripakdeevong, P.1
Cevec, M.2
Chang, A.T.3
Erat, M.C.4
Ziegeler, M.5
Zhao, Q.6
-
32
-
-
84908122152
-
High-throughput mutate-map-rescue evaluates SHAPE-directed RNA structure and uncovers excited states
-
S. Tian, P. Cordero, W. Kladwang, and R. Das High-throughput mutate-map-rescue evaluates SHAPE-directed RNA structure and uncovers excited states RNA 20 11 2014 1815 1826 10.1261/rna.044321.114
-
(2014)
RNA
, vol.20
, Issue.11
, pp. 1815-1826
-
-
Tian, S.1
Cordero, P.2
Kladwang, W.3
Das, R.4
-
33
-
-
0005822936
-
Improved estimation of secondary structure in ribonucleic acids
-
I. Tinoco Jr., P.N. Borer, B. Dengler, M.D. Levin, O.C. Uhlenbeck, and D.M. Crothers Improved estimation of secondary structure in ribonucleic acids Nature: New Biology 246 150 1973 40 41
-
(1973)
Nature: New Biology
, vol.246
, Issue.150
, pp. 40-41
-
-
Tinoco, Jr.I.1
Borer, P.N.2
Dengler, B.3
Levin, M.D.4
Uhlenbeck, O.C.5
Crothers, D.M.6
-
34
-
-
84922482101
-
RNA regulons in Hox 5' UTRs confer ribosome specificity to gene regulation
-
S. Xue, S. Tian, K. Fujii, W. Kladwang, R. Das, and M. Barna RNA regulons in Hox 5' UTRs confer ribosome specificity to gene regulation Nature 2014 10.1038/nature14010
-
(2014)
Nature
-
-
Xue, S.1
Tian, S.2
Fujii, K.3
Kladwang, W.4
Das, R.5
Barna, M.6
-
35
-
-
79959458096
-
HiTRACE: High-throughput robust analysis for capillary electrophoresis
-
S. Yoon, J. Kim, J. Hum, H. Kim, S. Park, and W. Kladwang HiTRACE: High-throughput robust analysis for capillary electrophoresis Bioinformatics 27 13 2011 1798 1805 10.1093/bioinformatics/btr277
-
(2011)
Bioinformatics
, vol.27
, Issue.13
, pp. 1798-1805
-
-
Yoon, S.1
Kim, J.2
Hum, J.3
Kim, H.4
Park, S.5
Kladwang, W.6
|