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Links from PubMed

Items: 16

1.

Using homology relations within a database markedly boosts protein sequence similarity search.

Tong J, Sadreyev RI, Pei J, Kinch LN, Grishin NV.

Proc Natl Acad Sci U S A. 2015 Jun 2;112(22):7003-8. doi: 10.1073/pnas.1424324112. Epub 2015 May 18.

2.

Bacillus anthracis pXO1 plasmid encodes a putative membrane-bound bacteriocin.

Perlińska A, Grynberg M.

PeerJ. 2014 Nov 20;2:e679. doi: 10.7717/peerj.679. eCollection 2014.

3.

From local structure to a global framework: recognition of protein folds.

Joseph AP, de Brevern AG.

J R Soc Interface. 2014 Apr 16;11(95):20131147. doi: 10.1098/rsif.2013.1147. Print 2014 Jun 6. Review.

4.

Bioinformatics analysis identify novel OB fold protein coding genes in C. elegans.

Dargahi D, Baillie D, Pio F.

PLoS One. 2013 Apr 25;8(4):e62204. doi: 10.1371/journal.pone.0062204. Print 2013.

5.

Conotoxin protein classification using free scores of words and support vector machines.

Zaki N, Wolfsheimer S, Nuel G, Khuri S.

BMC Bioinformatics. 2011 May 29;12:217. doi: 10.1186/1471-2105-12-217.

6.

Of bits and bugs--on the use of bioinformatics and a bacterial crystal structure to solve a eukaryotic repeat-protein structure.

Graebsch A, Roche S, Kostrewa D, Söding J, Niessing D.

PLoS One. 2010 Oct 14;5(10):e13402. doi: 10.1371/journal.pone.0013402.

7.

The CATH database.

Knudsen M, Wiuf C.

Hum Genomics. 2010 Feb;4(3):207-12.

8.

DescFold: a web server for protein fold recognition.

Yan RX, Si JN, Wang C, Zhang Z.

BMC Bioinformatics. 2009 Dec 14;10:416. doi: 10.1186/1471-2105-10-416.

9.

Structure prediction for CASP8 with all-atom refinement using Rosetta.

Raman S, Vernon R, Thompson J, Tyka M, Sadreyev R, Pei J, Kim D, Kellogg E, DiMaio F, Lange O, Kinch L, Sheffler W, Kim BH, Das R, Grishin NV, Baker D.

Proteins. 2009;77 Suppl 9:89-99. doi: 10.1002/prot.22540.

10.

Overlapping genes produce proteins with unusual sequence properties and offer insight into de novo protein creation.

Rancurel C, Khosravi M, Dunker AK, Romero PR, Karlin D.

J Virol. 2009 Oct;83(20):10719-36. doi: 10.1128/JVI.00595-09. Epub 2009 Jul 29.

11.

Fido, a novel AMPylation domain common to fic, doc, and AvrB.

Kinch LN, Yarbrough ML, Orth K, Grishin NV.

PLoS One. 2009 Jun 5;4(6):e5818. doi: 10.1371/journal.pone.0005818.

12.

COMPASS server for homology detection: improved statistical accuracy, speed and functionality.

Sadreyev RI, Tang M, Kim BH, Grishin NV.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W90-4. doi: 10.1093/nar/gkp360. Epub 2009 May 12.

13.

webPRC: the Profile Comparer for alignment-based searching of public domain databases.

Brandt BW, Heringa J.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W48-52. doi: 10.1093/nar/gkp279. Epub 2009 May 6.

14.

HorA web server to infer homology between proteins using sequence and structural similarity.

Kim BH, Cheng H, Grishin NV.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W532-8. doi: 10.1093/nar/gkp328. Epub 2009 May 5.

15.

The human Ago2 MC region does not contain an eIF4E-like mRNA cap binding motif.

Kinch LN, Grishin NV.

Biol Direct. 2009 Jan 21;4:2. doi: 10.1186/1745-6150-4-2.

16.

Accurate statistical model of comparison between multiple sequence alignments.

Sadreyev RI, Grishin NV.

Nucleic Acids Res. 2008 Apr;36(7):2240-8. doi: 10.1093/nar/gkn065. Epub 2008 Feb 19.

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