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Functional Annotations of Paralogs: A Blessing and a Curse.

Zallot R, Harrison KJ, Kolaczkowski B, de Crécy-Lagard V.

Life (Basel). 2016 Sep 8;6(3). pii: E39. doi: 10.3390/life6030039.


High quality draft genome sequence and analysis of Pontibacter roseus type strain SRC-1(T) (DSM 17521(T)) isolated from muddy waters of a drainage system in Chandigarh, India.

Mukherjee S, Lapidus A, Shapiro N, Cheng JF, Han J, Reddy T, Huntemann M, Ivanova N, Mikhailova N, Chen A, Palaniappan K, Spring S, Göker M, Markowitz V, Woyke T, Tindall BJ, Klenk HP, Kyrpides NC, Pati A.

Stand Genomic Sci. 2015 Feb 9;10:8. doi: 10.1186/1944-3277-10-8. eCollection 2015.


Structure-guided functional characterization of enediyne self-sacrifice resistance proteins, CalU16 and CalU19.

Elshahawi SI, Ramelot TA, Seetharaman J, Chen J, Singh S, Yang Y, Pederson K, Kharel MK, Xiao R, Lew S, Yennamalli RM, Miller MD, Wang F, Tong L, Montelione GT, Kennedy MA, Bingman CA, Zhu H, Phillips GN Jr, Thorson JS.

ACS Chem Biol. 2014 Oct 17;9(10):2347-58. doi: 10.1021/cb500327m. Epub 2014 Aug 13.


An introduction to sequence similarity ("homology") searching.

Pearson WR.

Curr Protoc Bioinformatics. 2013 Jun;Chapter 3:Unit3.1. doi: 10.1002/0471250953.bi0301s42. Review.


Functional classification of immune regulatory proteins.

Rubinstein R, Ramagopal UA, Nathenson SG, Almo SC, Fiser A.

Structure. 2013 May 7;21(5):766-76. doi: 10.1016/j.str.2013.02.022. Epub 2013 Apr 11.


Assignment of pterin deaminase activity to an enzyme of unknown function guided by homology modeling and docking.

Fan H, Hitchcock DS, Seidel RD 2nd, Hillerich B, Lin H, Almo SC, Sali A, Shoichet BK, Raushel FM.

J Am Chem Soc. 2013 Jan 16;135(2):795-803. doi: 10.1021/ja309680b. Epub 2013 Jan 2.


The Schistosoma mansoni phylome: using evolutionary genomics to gain insight into a parasite's biology.

Silva LL, Marcet-Houben M, Nahum LA, Zerlotini A, Gabaldón T, Oliveira G.

BMC Genomics. 2012 Nov 13;13:617. doi: 10.1186/1471-2164-13-617.


Mycobacterium tuberculosis Rv2419c, the missing glucosyl-3-phosphoglycerate phosphatase for the second step in methylglucose lipopolysaccharide biosynthesis.

Mendes V, Maranha A, Alarico S, da Costa MS, Empadinhas N.

Sci Rep. 2011;1:177. doi: 10.1038/srep00177. Epub 2011 Nov 30.


Remote thioredoxin recognition using evolutionary conservation and structural dynamics.

Tang GW, Altman RB.

Structure. 2011 Apr 13;19(4):461-70. doi: 10.1016/j.str.2011.02.007.


Searching the protein structure database for ligand-binding site similarities using CPASS v.2.

Powers R, Copeland JC, Stark JL, Caprez A, Guru A, Swanson D.

BMC Res Notes. 2011 Jan 26;4:17. doi: 10.1186/1756-0500-4-17.


Predicting DNA-binding specificities of eukaryotic transcription factors.

Schröder A, Eichner J, Supper J, Eichner J, Wanke D, Henneges C, Zell A.

PLoS One. 2010 Nov 30;5(11):e13876. doi: 10.1371/journal.pone.0013876.


Knowledge-based annotation of small molecule binding sites in proteins.

Thangudu RR, Tyagi M, Shoemaker BA, Bryant SH, Panchenko AR, Madej T.

BMC Bioinformatics. 2010 Jul 1;11:365. doi: 10.1186/1471-2105-11-365.


Evolutionary trace annotation of protein function in the structural proteome.

Erdin S, Ward RM, Venner E, Lichtarge O.

J Mol Biol. 2010 Mar 12;396(5):1451-73. doi: 10.1016/j.jmb.2009.12.037. Epub 2009 Dec 28.


Inferred Biomolecular Interaction Server--a web server to analyze and predict protein interacting partners and binding sites.

Shoemaker BA, Zhang D, Thangudu RR, Tyagi M, Fong JH, Marchler-Bauer A, Bryant SH, Madej T, Panchenko AR.

Nucleic Acids Res. 2010 Jan;38(Database issue):D518-24. doi: 10.1093/nar/gkp842. Epub 2009 Oct 20.


A comprehensive analysis of gene expression evolution between humans and mice.

Wang Y, Rekaya R.

Evol Bioinform Online. 2009 Jul 6;5:81-90.


EFICAz2: enzyme function inference by a combined approach enhanced by machine learning.

Arakaki AK, Huang Y, Skolnick J.

BMC Bioinformatics. 2009 Apr 13;10:107. doi: 10.1186/1471-2105-10-107.


Functional annotation of two new carboxypeptidases from the amidohydrolase superfamily of enzymes.

Xiang DF, Xu C, Kumaran D, Brown AC, Sauder JM, Burley SK, Swaminathan S, Raushel FM.

Biochemistry. 2009 Jun 2;48(21):4567-76. doi: 10.1021/bi900453u.


FINDSITE: a combined evolution/structure-based approach to protein function prediction.

Skolnick J, Brylinski M.

Brief Bioinform. 2009 Jul;10(4):378-91. doi: 10.1093/bib/bbp017. Epub 2009 Mar 26. Review.


Evolutionary Trace Annotation Server: automated enzyme function prediction in protein structures using 3D templates.

Ward RM, Venner E, Daines B, Murray S, Erdin S, Kristensen DM, Lichtarge O.

Bioinformatics. 2009 Jun 1;25(11):1426-7. doi: 10.1093/bioinformatics/btp160. Epub 2009 Mar 23.

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