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Items: 15


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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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