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Items: 1 to 20 of 87

1.

Accurate protein structure annotation through competitive diffusion of enzymatic functions over a network of local evolutionary similarities.

Venner E, Lisewski AM, Erdin S, Ward RM, Amin SR, Lichtarge O.

PLoS One. 2010 Dec 13;5(12):e14286. doi: 10.1371/journal.pone.0014286.

2.

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.

3.

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.

4.

ETAscape: analyzing protein networks to predict enzymatic function and substrates in Cytoscape.

Bachman BJ, Venner E, Lua RC, Erdin S, Lichtarge O.

Bioinformatics. 2012 Aug 15;28(16):2186-8. doi: 10.1093/bioinformatics/bts331. Epub 2012 Jun 11.

5.

Prediction of enzyme function based on 3D templates of evolutionarily important amino acids.

Kristensen DM, Ward RM, Lisewski AM, Erdin S, Chen BY, Fofanov VY, Kimmel M, Kavraki LE, Lichtarge O.

BMC Bioinformatics. 2008 Jan 11;9:17. doi: 10.1186/1471-2105-9-17.

6.

Function prediction from networks of local evolutionary similarity in protein structure.

Erdin S, Venner E, Lisewski AM, Lichtarge O.

BMC Bioinformatics. 2013;14 Suppl 3:S6. doi: 10.1186/1471-2105-14-S3-S6. Epub 2013 Feb 28.

7.

De-orphaning the structural proteome through reciprocal comparison of evolutionarily important structural features.

Ward RM, Erdin S, Tran TA, Kristensen DM, Lisewski AM, Lichtarge O.

PLoS One. 2008 May 7;3(5):e2136. doi: 10.1371/journal.pone.0002136.

8.

Prediction and experimental validation of enzyme substrate specificity in protein structures.

Amin SR, Erdin S, Ward RM, Lua RC, Lichtarge O.

Proc Natl Acad Sci U S A. 2013 Nov 5;110(45):E4195-202. doi: 10.1073/pnas.1305162110. Epub 2013 Oct 21.

9.

Evolutionary cores of domain co-occurrence networks.

Wuchty S, Almaas E.

BMC Evol Biol. 2005 Mar 23;5:24.

10.
11.

Cross-organism learning method to discover new gene functionalities.

Domeniconi G, Masseroli M, Moro G, Pinoli P.

Comput Methods Programs Biomed. 2016 Apr;126:20-34. doi: 10.1016/j.cmpb.2015.12.002. Epub 2015 Dec 17.

PMID:
26724853
12.

Statistically rigorous automated protein annotation.

Krebs WG, Bourne PE.

Bioinformatics. 2004 May 1;20(7):1066-73. Epub 2004 Feb 5.

PMID:
14764575
13.

Resolving protein structure-function-binding site relationships from a binding site similarity network perspective.

Mudgal R, Srinivasan N, Chandra N.

Proteins. 2017 Jul;85(7):1319-1335. doi: 10.1002/prot.25293. Epub 2017 Apr 22.

PMID:
28342236
14.

Assigning new GO annotations to protein data bank sequences by combining structure and sequence homology.

Ponomarenko JV, Bourne PE, Shindyalov IN.

Proteins. 2005 Mar 1;58(4):855-65.

PMID:
15645518
15.

Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps.

Nabieva E, Jim K, Agarwal A, Chazelle B, Singh M.

Bioinformatics. 2005 Jun;21 Suppl 1:i302-10.

PMID:
15961472
16.

Target space for structural genomics revisited.

Liu J, Rost B.

Bioinformatics. 2002 Jul;18(7):922-33.

PMID:
12117789
17.

Quantification of the impact of PSI:Biology according to the annotations of the determined structures.

DePietro PJ, Julfayev ES, McLaughlin WA.

BMC Struct Biol. 2013 Oct 21;13:24. doi: 10.1186/1472-6807-13-24.

18.

ELISA: structure-function inferences based on statistically significant and evolutionarily inspired observations.

Shakhnovich BE, Harvey JM, Comeau S, Lorenz D, DeLisi C, Shakhnovich E.

BMC Bioinformatics. 2003 Sep 2;4:34. Epub 2003 Sep 2.

19.

Sequence and structure continuity of evolutionary importance improves protein functional site discovery and annotation.

Wilkins AD, Lua R, Erdin S, Ward RM, Lichtarge O.

Protein Sci. 2010 Jul;19(7):1296-311. doi: 10.1002/pro.406.

20.

UET: a database of evolutionarily-predicted functional determinants of protein sequences that cluster as functional sites in protein structures.

Lua RC, Wilson SJ, Konecki DM, Wilkins AD, Venner E, Morgan DH, Lichtarge O.

Nucleic Acids Res. 2016 Jan 4;44(D1):D308-12. doi: 10.1093/nar/gkv1279. Epub 2015 Nov 20.

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