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Items: 15

1.

The Recipe for Protein Sequence-Based Function Prediction and Its Implementation in the ANNOTATOR Software Environment.

Eisenhaber B, Kuchibhatla D, Sherman W, Sirota FL, Berezovsky IN, Wong WC, Eisenhaber F.

Methods Mol Biol. 2016;1415:477-506. doi: 10.1007/978-1-4939-3572-7_25.

PMID:
27115649
2.

Single-residue posttranslational modification sites at the N-terminus, C-terminus or in-between: To be or not to be exposed for enzyme access.

Sirota FL, Maurer-Stroh S, Eisenhaber B, Eisenhaber F.

Proteomics. 2015 Jul;15(14):2525-46. doi: 10.1002/pmic.201400633.

3.

Conservation of the extended substrate specificity profiles among homologous granzymes across species.

Plasman K, Maurer-Stroh S, Ahmad J, Hao H, Kaiserman D, Sirota FL, Jonckheere V, Bird PI, Gevaert K, Van Damme P.

Mol Cell Proteomics. 2013 Oct;12(10):2921-34. doi: 10.1074/mcp.M113.028670.

4.

Beware of moving targets: reference proteome content fluctuates substantially over the years.

Sirota FL, Batagov A, Schneider G, Eisenhaber B, Eisenhaber F, Maurer-Stroh S.

J Bioinform Comput Biol. 2012 Dec;10(6):1250020. doi: 10.1142/S0219720012500205.

PMID:
22867629
5.

Tachyon search speeds up retrieval of similar sequences by several orders of magnitude.

Tan J, Kuchibhatla D, Sirota FL, Sherman WA, Gattermayer T, Kwoh CY, Eisenhaber F, Schneider G, Maurer-Stroh S.

Bioinformatics. 2012 Jun 15;28(12):1645-6. doi: 10.1093/bioinformatics/bts197.

6.

All that glitters is not gold--founder effects complicate associations of flu mutations to disease severity.

Lee RT, Santos CL, de Paiva TM, Cui L, Sirota FL, Eisenhaber F, Maurer-Stroh S.

Virol J. 2010 Nov 1;7:297. doi: 10.1186/1743-422X-7-297.

7.

Integrated tools for biomolecular sequence-based function prediction as exemplified by the ANNOTATOR software environment.

Schneider G, Wildpaner M, Sirota FL, Maurer-Stroh S, Eisenhaber B, Eisenhaber F.

Methods Mol Biol. 2010;609:257-67. doi: 10.1007/978-1-60327-241-4_15.

PMID:
20221924
8.

Parameterization of disorder predictors for large-scale applications requiring high specificity by using an extended benchmark dataset.

Sirota FL, Ooi HS, Gattermayer T, Schneider G, Eisenhaber F, Maurer-Stroh S.

BMC Genomics. 2010 Feb 10;11 Suppl 1:S15. doi: 10.1186/1471-2164-11-S1-S15.

9.

Mapping the sequence mutations of the 2009 H1N1 influenza A virus neuraminidase relative to drug and antibody binding sites.

Maurer-Stroh S, Ma J, Lee RT, Sirota FL, Eisenhaber F.

Biol Direct. 2009 May 20;4:18; discussion 18. doi: 10.1186/1745-6150-4-18.

10.

ANNIE: integrated de novo protein sequence annotation.

Ooi HS, Kwo CY, Wildpaner M, Sirota FL, Eisenhaber B, Maurer-Stroh S, Wong WC, Schleiffer A, Eisenhaber F, Schneider G.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W435-40. doi: 10.1093/nar/gkp254.

11.

Mechanism and energy landscape of domain swapping in the B1 domain of protein G.

Malevanets A, Sirota FL, Wodak SJ.

J Mol Biol. 2008 Sep 26;382(1):223-35. doi: 10.1016/j.jmb.2008.06.025.

PMID:
18588900
12.

Role of the amino acid sequence in domain swapping of the B1 domain of protein G.

Sirota FL, Héry-Huynh S, Maurer-Stroh S, Wodak SJ.

Proteins. 2008 Jul;72(1):88-104. doi: 10.1002/prot.21901.

PMID:
18186476
13.

Towards complete sets of farnesylated and geranylgeranylated proteins.

Maurer-Stroh S, Koranda M, Benetka W, Schneider G, Sirota FL, Eisenhaber F.

PLoS Comput Biol. 2007 Apr 6;3(4):e66.

14.

MYRbase: analysis of genome-wide glycine myristoylation enlarges the functional spectrum of eukaryotic myristoylated proteins.

Maurer-Stroh S, Gouda M, Novatchkova M, Schleiffer A, Schneider G, Sirota FL, Wildpaner M, Hayashi N, Eisenhaber F.

Genome Biol. 2004;5(3):R21.

15.

Molecular modeling and dynamics of the sodium channel inactivation gate.

Sirota FL, Pascutti PG, Anteneodo C.

Biophys J. 2002 Mar;82(3):1207-15.

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