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Items: 15


Phylogenetic Analysis with Improved Parameters Reveals Conservation in lncRNA Structures.

Tavares RCA, Pyle AM, Somarowthu S.

J Mol Biol. 2019 Apr 5;431(8):1592-1603. doi: 10.1016/j.jmb.2019.03.012. Epub 2019 Mar 16.


Visualizing the secondary and tertiary architectural domains of lncRNA RepA.

Liu F, Somarowthu S, Pyle AM.

Nat Chem Biol. 2017 Mar;13(3):282-289. doi: 10.1038/nchembio.2272. Epub 2017 Jan 9.


Progress and Current Challenges in Modeling Large RNAs.

Somarowthu S.

J Mol Biol. 2016 Feb 27;428(5 Pt A):736-747. doi: 10.1016/j.jmb.2015.11.011. Epub 2015 Nov 14. Review.


Native Purification and Analysis of Long RNAs.

Chillón I, Marcia M, Legiewicz M, Liu F, Somarowthu S, Pyle AM.

Methods Enzymol. 2015;558:3-37. doi: 10.1016/bs.mie.2015.01.008. Epub 2015 Feb 27.


HOTAIR forms an intricate and modular secondary structure.

Somarowthu S, Legiewicz M, Chillón I, Marcia M, Liu F, Pyle AM.

Mol Cell. 2015 Apr 16;58(2):353-61. doi: 10.1016/j.molcel.2015.03.006. Epub 2015 Apr 9.


Prediction of distal residue participation in enzyme catalysis.

Brodkin HR, DeLateur NA, Somarowthu S, Mills CL, Novak WR, Beuning PJ, Ringe D, Ondrechen MJ.

Protein Sci. 2015 May;24(5):762-78. doi: 10.1002/pro.2648. Epub 2015 Apr 2.


Visualizing the ai5γ group IIB intron.

Somarowthu S, Legiewicz M, Keating KS, Pyle AM.

Nucleic Acids Res. 2014 Feb;42(3):1947-58. doi: 10.1093/nar/gkt1051. Epub 2013 Nov 6.


Solving nucleic acid structures by molecular replacement: examples from group II intron studies.

Marcia M, Humphris-Narayanan E, Keating KS, Somarowthu S, Rajashankar K, Pyle AM.

Acta Crystallogr D Biol Crystallogr. 2013 Nov;69(Pt 11):2174-85. doi: 10.1107/S0907444913013218. Epub 2013 Oct 12. Review.


Now on display: a gallery of group II intron structures at different stages of catalysis.

Marcia M, Somarowthu S, Pyle AM.

Mob DNA. 2013 May 1;4(1):14. doi: 10.1186/1759-8753-4-14.


Protein function annotation with Structurally Aligned Local Sites of Activity (SALSAs).

Wang Z, Yin P, Lee JS, Parasuram R, Somarowthu S, Ondrechen MJ.

BMC Bioinformatics. 2013;14 Suppl 3:S13. doi: 10.1186/1471-2105-14-S3-S13. Epub 2013 Feb 28.


POOL server: machine learning application for functional site prediction in proteins.

Somarowthu S, Ondrechen MJ.

Bioinformatics. 2012 Aug 1;28(15):2078-9. doi: 10.1093/bioinformatics/bts321. Epub 2012 Jun 1.


A tale of two isomerases: compact versus extended active sites in ketosteroid isomerase and phosphoglucose isomerase.

Somarowthu S, Brodkin HR, D'Aquino JA, Ringe D, Ondrechen MJ, Beuning PJ.

Biochemistry. 2011 Nov 1;50(43):9283-95. doi: 10.1021/bi201089v. Epub 2011 Oct 4.


Crystal structure of a metal-dependent phosphoesterase (YP_910028.1) from Bifidobacterium adolescentis: Computational prediction and experimental validation of phosphoesterase activity.

Han GW, Ko J, Farr CL, Deller MC, Xu Q, Chiu HJ, Miller MD, Sefcikova J, Somarowthu S, Beuning PJ, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA, Ondrechen MJ.

Proteins. 2011 Jul;79(7):2146-60. doi: 10.1002/prot.23035. Epub 2011 May 2.


High-performance prediction of functional residues in proteins with machine learning and computed input features.

Somarowthu S, Yang H, Hildebrand DG, Ondrechen MJ.

Biopolymers. 2011 Jun;95(6):390-400. doi: 10.1002/bip.21589.


Functional classification of protein 3D structures from predicted local interaction sites.

Parasuram R, Lee JS, Yin P, Somarowthu S, Ondrechen MJ.

J Bioinform Comput Biol. 2010 Dec;8 Suppl 1:1-15.


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