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Birgit Eisenhaber - Publications

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56 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Cserző M, Eisenhaber B, Eisenhaber F, Magyar C, Simon I. The First Quarter Century of the Dense Alignment Surface Transmembrane Prediction Method. International Journal of Molecular Sciences. 24. PMID 37762320 DOI: 10.3390/ijms241814016  0.313
2021 Sirota FL, Maurer-Stroh S, Li Z, Eisenhaber F, Eisenhaber B. Functional Classification of Super-Large Families of Enzymes Based on Substrate Binding Pocket Residues for Biocatalysis and Enzyme Engineering Applications. Frontiers in Bioengineering and Biotechnology. 9: 701120. PMID 34409021 DOI: 10.3389/fbioe.2021.701120  0.327
2021 Eisenhaber B, Sinha S, Jadalanki CK, Shitov VA, Tan QW, Sirota FL, Eisenhaber F. Conserved sequence motifs in human TMTC1, TMTC2, TMTC3, and TMTC4, new O-mannosyltransferases from the GT-C/PMT clan, are rationalized as ligand binding sites. Biology Direct. 16: 4. PMID 33436046 DOI: 10.1186/s13062-021-00291-w  0.393
2020 Su CT, Sinha S, Eisenhaber B, Eisenhaber F. Structural modelling of the lumenal domain of human GPAA1, the metallo-peptide synthetase subunit of the transamidase complex, reveals zinc-binding mode and two flaps surrounding the active site. Biology Direct. 15: 14. PMID 32993792 DOI: 10.1186/s13062-020-00266-3  0.318
2019 Eisenhaber B, Eisenhaber F. Darkness in the human gene and protein function space despite big omics data and decline in molecular mechanism discovery after 2000 Acta Crystallographica Section A. 75. DOI: 10.1107/S2053273319093756  0.305
2018 Eisenhaber B, Sinha S, Wong WC, Eisenhaber F. Function of a membrane-embedded domain evolutionarily multiplied in the GPI lipid anchor pathway proteins PIG-B, PIG-M, PIG-U, PIG-W, PIG-V, and PIG-Z. Cell Cycle (Georgetown, Tex.). 1-7. PMID 29764287 DOI: 10.1080/15384101.2018.1456294  0.35
2017 Marakasova ES, Eisenhaber B, Maurer-Stroh S, Eisenhaber F, Baranova A. Prenylation of viral proteins by enzymes of the host: Virus-driven rationale for therapy with statins and FT/GGT1 inhibitors. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. PMID 28885709 DOI: 10.1002/Bies.201700014  0.334
2017 Baker JA, Wong WC, Eisenhaber B, Warwicker J, Eisenhaber F. Charged residues next to transmembrane regions revisited: "Positive-inside rule" is complemented by the "negative inside depletion/outside enrichment rule". Bmc Biology. 15: 66. PMID 28738801 DOI: 10.1186/S12915-017-0404-4  0.428
2017 Kamariah N, Eisenhaber B, Eisenhaber F, Gruber G. Essential role of the flexible linker on the conformational equilibrium of bacterial peroxiredoxin reductase for effective regeneration of peroxiredoxin. The Journal of Biological Chemistry. PMID 28270505 DOI: 10.1074/Jbc.M117.775858  0.367
2017 Lua WH, Ling WL, Su CT, Yeo JY, Verma CS, Eisenhaber B, Eisenhaber F, Gan SK. Discovery of a novel splice variant of Fcar (CD89) unravels sequence segments necessary for efficient secretion: a story of bad signal peptides and good ones that nevertheless do not make it. Cell Cycle (Georgetown, Tex.). 0. PMID 28103138 DOI: 10.1080/15384101.2017.1281480  0.367
2016 Yap CK, Eisenhaber B, Eisenhaber F, Wong WC. xHMMER3x2: Utilizing HMMER3's speed and HMMER2's sensitivity and specificity in the glocal alignment mode for improved large-scale protein domain annotation. Biology Direct. 11: 63. PMID 27894340 DOI: 10.1186/S13062-016-0163-0  0.338
2016 Kamariah N, Sek MF, Eisenhaber B, Eisenhaber F, Grüber G. Transition steps in peroxide reduction and a molecular switch for peroxide robustness of prokaryotic peroxiredoxins. Scientific Reports. 6: 37610. PMID 27892488 DOI: 10.1038/Srep37610  0.349
2016 Berezovsky IN, Guarnera E, Zheng Z, Eisenhaber B, Eisenhaber F. Protein function machinery: from basic structural units to modulation of activity. Current Opinion in Structural Biology. 42: 67-74. PMID 27865209 DOI: 10.1016/J.Sbi.2016.10.021  0.415
2016 Eisenhaber B, Kuchibhatla D, Sherman W, Sirota FL, Berezovsky IN, Wong WC, Eisenhaber F. The Recipe for Protein Sequence-Based Function Prediction and Its Implementation in the ANNOTATOR Software Environment. Methods in Molecular Biology (Clifton, N.J.). 1415: 477-506. PMID 27115649 DOI: 10.1007/978-1-4939-3572-7_25  0.467
2015 Kamariah N, Nartey W, Eisenhaber B, Eisenhaber F, Grüber G. Low resolution solution structure of an enzymatic active AhpC10:AhpF2 ensemble of the Escherichia coli Alkyl hydroperoxide Reductase. Journal of Structural Biology. PMID 26584540 DOI: 10.1016/J.Jsb.2015.11.004  0.384
2015 Sherman WA, Kuchibhatla DB, Limviphuvadh V, Maurer-Stroh S, Eisenhaber B, Eisenhaber F. HPMV: Human protein mutation viewer - relating sequence mutations to protein sequence architecture and function changes. Journal of Bioinformatics and Computational Biology. 13: 1550028. PMID 26503432 DOI: 10.1142/S0219720015500286  0.41
2015 Nartey W, Basak S, Kamariah N, Manimekalai MS, Robson S, Wagner G, Eisenhaber B, Eisenhaber F, Grüber G. NMR studies reveal a novel grab and release mechanism for efficient catalysis of the bacterial 2-Cys peroxiredoxin machinery. The Febs Journal. PMID 26402142 DOI: 10.1111/Febs.13522  0.338
2015 Wong WC, Yap CK, Eisenhaber B, Eisenhaber F. dissectHMMER: a HMMER-based score dissection framework that statistically evaluates fold-critical sequence segments for domain fold similarity. Biology Direct. 10: 39. PMID 26228544 DOI: 10.1186/S13062-015-0068-3  0.492
2015 Kamariah N, Manimekalai MS, Nartey W, Eisenhaber F, Eisenhaber B, Grüber G. Crystallographic and solution studies of NAD(+)- and NADH-bond alkylhydroperoxide reductase subunit F (AhpF) from Escherichia coli provide insight into sequential enzymatic steps. Biochimica Et Biophysica Acta. PMID 26092085 DOI: 10.1016/J.Bbabio.2015.06.011  0.362
2015 Sirota FL, Maurer-Stroh S, Eisenhaber B, Eisenhaber F. Single-residue posttranslational modification sites at the N-terminus, C-terminus or in-between: To be or not to be exposed for enzyme access. Proteomics. PMID 26038108 DOI: 10.1002/Pmic.201400633  0.493
2014 Dip PV, Kamariah N, Subramanian Manimekalai MS, Nartey W, Balakrishna AM, Eisenhaber F, Eisenhaber B, Grüber G. Structure, mechanism and ensemble formation of the alkylhydroperoxide reductase subunits AhpC and AhpF from Escherichia coli. Acta Crystallographica. Section D, Biological Crystallography. 70: 2848-62. PMID 25372677 DOI: 10.1107/S1399004714019233  0.331
2014 Dip PV, Kamariah N, Nartey W, Beushausen C, Kostyuchenko VA, Ng TS, Lok SM, Saw WG, Eisenhaber F, Eisenhaber B, Grüber G. Key roles of the Escherichia coli AhpC C-terminus in assembly and catalysis of alkylhydroperoxide reductase, an enzyme essential for the alleviation of oxidative stress. Biochimica Et Biophysica Acta. 1837: 1932-43. PMID 25193562 DOI: 10.1016/J.Bbabio.2014.08.007  0.375
2014 Wong WC, Maurer-Stroh S, Eisenhaber B, Eisenhaber F. On the necessity of dissecting sequence similarity scores into segment-specific contributions for inferring protein homology, function prediction and annotation. Bmc Bioinformatics. 15: 166. PMID 24890864 DOI: 10.1186/1471-2105-15-166  0.489
2014 Eisenhaber B, Eisenhaber S, Kwang TY, Grüber G, Eisenhaber F. Transamidase subunit GAA1/GPAA1 is a M28 family metallo-peptide-synthetase that catalyzes the peptide bond formation between the substrate protein's omega-site and the GPI lipid anchor's phosphoethanolamine. Cell Cycle (Georgetown, Tex.). 13: 1912-7. PMID 24743167 DOI: 10.4161/Cc.28761  0.343
2014 Kuchibhatla DB, Sherman WA, Chung BY, Cook S, Schneider G, Eisenhaber B, Karlin DG. Powerful sequence similarity search methods and in-depth manual analyses can identify remote homologs in many apparently "orphan" viral proteins. Journal of Virology. 88: 10-20. PMID 24155369 DOI: 10.1128/Jvi.02595-13  0.463
2013 Goncearenco A, Mitternacht S, Yong T, Eisenhaber B, Eisenhaber F, Berezovsky IN. SPACER: Server for predicting allosteric communication and effects of regulation. Nucleic Acids Research. 41: W266-72. PMID 23737445 DOI: 10.1093/Nar/Gkt460  0.357
2013 Saw WG, Eisenhaber B, Eisenhaber F, Grüber G. Low-resolution structure of the soluble domain GPAA1 (yGPAA170-247) of the glycosylphosphatidylinositol transamidase subunit GPAA1 from Saccharomyces cerevisiae. Bioscience Reports. 33: e00033. PMID 23458223 DOI: 10.1042/Bsr20120107  0.355
2012 Sirota FL, Batagov A, Schneider G, Eisenhaber B, Eisenhaber F, Maurer-Stroh S. Beware of moving targets: reference proteome content fluctuates substantially over the years. Journal of Bioinformatics and Computational Biology. 10: 1250020. PMID 22867629 DOI: 10.1142/S0219720012500205  0.422
2011 Eisenhaber B, Sammer M, Lua WH, Benetka W, Liew LL, Yu W, Lee HK, Koranda M, Eisenhaber F, Adhikari S. Nuclear import of a lipid-modified transcription factor: mobilization of NFAT5 isoform a by osmotic stress. Cell Cycle (Georgetown, Tex.). 10: 3897-911. PMID 22071693 DOI: 10.4161/Cc.10.22.18043  0.308
2011 Kamariah N, Eisenhaber F, Adhikari S, Eisenhaber B, Grüber G. Purification and crystallization of yeast glycosylphosphatidylinositol transamidase subunit PIG-S (PIG-S(71-467)). Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. 67: 896-9. PMID 21821889 DOI: 10.1107/S1744309111024080  0.367
2011 Toh YK, Kamariah N, Maurer-Stroh S, Roessle M, Eisenhaber F, Adhikari S, Eisenhaber B, Grüber G. Structural insight into the glycosylphosphatidylinositol transamidase subunits PIG-K and PIG-S from yeast. Journal of Structural Biology. 173: 271-81. PMID 21134462 DOI: 10.1016/J.Jsb.2010.11.026  0.323
2010 Eisenhaber B, Eisenhaber F. Prediction of posttranslational modification of proteins from their amino acid sequence. Methods in Molecular Biology (Clifton, N.J.). 609: 365-84. PMID 20221930 DOI: 10.1007/978-1-60327-241-4_21  0.513
2010 Schneider G, Wildpaner M, Sirota FL, Maurer-Stroh S, Eisenhaber B, Eisenhaber F. Integrated tools for biomolecular sequence-based function prediction as exemplified by the ANNOTATOR software environment. Methods in Molecular Biology (Clifton, N.J.). 609: 257-67. PMID 20221924 DOI: 10.1007/978-1-60327-241-4_15  0.373
2010 Ooi HS, Schneider G, Chan YL, Lim TT, Eisenhaber B, Eisenhaber F. Databases of protein-protein interactions and complexes. Methods in Molecular Biology (Clifton, N.J.). 609: 145-59. PMID 20221918 DOI: 10.1007/978-1-60327-241-4_9  0.438
2009 Tse WK, Eisenhaber B, Ho SH, Ng Q, Eisenhaber F, Jiang YJ. Genome-wide loss-of-function analysis of deubiquitylating enzymes for zebrafish development. Bmc Genomics. 10: 637. PMID 20040115 DOI: 10.1186/1471-2164-10-637  0.363
2009 Ooi HS, Kwo CY, Wildpaner M, Sirota FL, Eisenhaber B, Maurer-Stroh S, Wong WC, Schleiffer A, Eisenhaber F, Schneider G. ANNIE: integrated de novo protein sequence annotation. Nucleic Acids Research. 37: W435-40. PMID 19389726 DOI: 10.1093/Nar/Gkp254  0.459
2007 Eisenhaber B, Eisenhaber F. Posttranslational modifications and subcellular localization signals: indicators of sequence regions without inherent 3D structure? Current Protein & Peptide Science. 8: 197-203. PMID 17430201 DOI: 10.2174/138920307780363424  0.519
2007 Eisenhaber B, Chumak N, Eisenhaber F, Hauser MT. The ring between ring fingers (RBR) protein family. Genome Biology. 8: 209. PMID 17367545 DOI: 10.1186/Gb-2007-8-3-209  0.416
2005 O'Connor E, Eisenhaber B, Dalley J, Wang T, Missen C, Bulleid N, Bishop PN, Trump D. Species specific membrane anchoring of nyctalopin, a small leucine-rich repeat protein. Human Molecular Genetics. 14: 1877-87. PMID 15905181 DOI: 10.1093/Hmg/Ddi194  0.3
2005 Novatchkova M, Bachmair A, Eisenhaber B, Eisenhaber F. Proteins with two SUMO-like domains in chromatin-associated complexes: the RENi (Rad60-Esc2-NIP45) family. Bmc Bioinformatics. 6: 22. PMID 15698469 DOI: 10.1186/1471-2105-6-22  0.442
2004 Eisenhaber B, Eisenhaber F, Maurer-Stroh S, Neuberger G. Prediction of sequence signals for lipid post-translational modifications: insights from case studies. Proteomics. 4: 1614-25. PMID 15174131 DOI: 10.1002/Pmic.200300781  0.498
2004 Eisenhaber B, Schneider G, Wildpaner M, Eisenhaber F. A sensitive predictor for potential GPI lipid modification sites in fungal protein sequences and its application to genome-wide studies for Aspergillus nidulans, Candida albicans, Neurospora crassa, Saccharomyces cerevisiae and Schizosaccharomyces pombe. Journal of Molecular Biology. 337: 243-53. PMID 15003443 DOI: 10.1016/J.Jmb.2004.01.025  0.505
2004 Cserzo M, Eisenhaber F, Eisenhaber B, Simon I. TM or not TM: transmembrane protein prediction with low false positive rate using DAS-TMfilter. Bioinformatics (Oxford, England). 20: 136-7. PMID 14693825 DOI: 10.1093/Bioinformatics/Btg394  0.316
2003 Eisenhaber B, Wildpaner M, Schultz CJ, Borner GH, Dupree P, Eisenhaber F. Glycosylphosphatidylinositol lipid anchoring of plant proteins. Sensitive prediction from sequence- and genome-wide studies for Arabidopsis and rice. Plant Physiology. 133: 1691-701. PMID 14681532 DOI: 10.1104/Pp.103.023580  0.388
2003 Eisenhaber F, Eisenhaber B, Kubina W, Maurer-Stroh S, Neuberger G, Schneider G, Wildpaner M. Prediction of lipid posttranslational modifications and localization signals from protein sequences: big-Pi, NMT and PTS1. Nucleic Acids Research. 31: 3631-4. PMID 12824382 DOI: 10.1093/Nar/Gkg537  0.49
2003 Neuberger G, Maurer-Stroh S, Eisenhaber B, Hartig A, Eisenhaber F. Prediction of peroxisomal targeting signal 1 containing proteins from amino acid sequence. Journal of Molecular Biology. 328: 581-92. PMID 12706718 DOI: 10.1016/S0022-2836(03)00319-X  0.484
2003 Neuberger G, Maurer-Stroh S, Eisenhaber B, Hartig A, Eisenhaber F. Motif refinement of the peroxisomal targeting signal 1 and evaluation of taxon-specific differences. Journal of Molecular Biology. 328: 567-79. PMID 12706717 DOI: 10.1016/S0022-2836(03)00318-8  0.477
2003 Eisenhaber B, Maurer-Stroh S, Novatchkova M, Schneider G, Eisenhaber F. Enzymes and auxiliary factors for GPI lipid anchor biosynthesis and post-translational transfer to proteins. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 25: 367-85. PMID 12655644 DOI: 10.1002/Bies.10254  0.48
2002 Cserzö M, Eisenhaber F, Eisenhaber B, Simon I. On filtering false positive transmembrane protein predictions. Protein Engineering. 15: 745-52. PMID 12456873 DOI: 10.1093/Protein/15.9.745  0.457
2002 Maurer-Stroh S, Eisenhaber B, Eisenhaber F. N-terminal N-myristoylation of proteins: prediction of substrate proteins from amino acid sequence. Journal of Molecular Biology. 317: 541-57. PMID 11955008 DOI: 10.1006/Jmbi.2002.5426  0.523
2002 Maurer-Stroh S, Eisenhaber B, Eisenhaber F. N-terminal N-myristoylation of proteins: refinement of the sequence motif and its taxon-specific differences. Journal of Molecular Biology. 317: 523-40. PMID 11955007 DOI: 10.1006/Jmbi.2002.5425  0.496
2001 Eisenhaber B, Bork P, Eisenhaber F. Post-translational GPI lipid anchor modification of proteins in kingdoms of life: analysis of protein sequence data from complete genomes. Protein Engineering. 14: 17-25. PMID 11287675 DOI: 10.1093/Protein/14.1.17  0.589
2000 Eisenhaber B, Bork P, Yuan Y, Löffler G, Eisenhaber F. Automated annotation of GPI anchor sites: case study C. elegans. Trends in Biochemical Sciences. 25: 340-1. PMID 10871885 DOI: 10.1016/S0968-0004(00)01601-7  0.448
1999 Eisenhaber B, Bork P, Eisenhaber F. Prediction of potential GPI-modification sites in proprotein sequences. Journal of Molecular Biology. 292: 741-58. PMID 10497036 DOI: 10.1006/Jmbi.1999.3069  0.595
1999 Sunyaev SR, Eisenhaber F, Rodchenkov IV, Eisenhaber B, Tumanyan VG, Kuznetsov EN. PSIC: profile extraction from sequence alignments with position-specific counts of independent observations. Protein Engineering. 12: 387-94. PMID 10360979 DOI: 10.1093/Protein/12.5.387  0.413
1998 Eisenhaber B, Bork P, Eisenhaber F. Sequence properties of GPI-anchored proteins near the omega-site: constraints for the polypeptide binding site of the putative transamidase. Protein Engineering. 11: 1155-61. PMID 9930665 DOI: 10.1093/Protein/11.12.1155  0.573
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