Staff Scientist (Akadem. Oberrat)
Interests
- Sequence Structure Function Relationship
- Effect of non-synonymous mutations
- Protein Evolution
Education
Dr. sc. hum. (PhD) in Bioinformatics, 2003
University of Heidelberg / EMBLDiplom in Biology, 1999
University of Göttingen
Publications
2022
- N. Ferruz, S. Schmidt, and B. Höcker, A deep unsupervised language model for protein design. bioRxiv, 2022. doi:10.1101/2022.03.09.483666
2021
- N. Ferruz, S. Schmidt, and B. Höcker,
ProteinTools: a toolkit to analyze protein structures,
Nucleic Acids Research, vol. 49, no. W1, pp. W559–W566, 2021. doi:10.1093/nar/gkab375 - N. Ferruz, F. Michel, F. Lobos, S. Schmidt, and B. Höcker,
Fuzzle 2.0: Ligand Binding in Natural Protein Building Blocks,
Frontiers in Molecular Biosciences, vol. 8, p. 715972, 2021. doi:10.3389/fmolb.2021.715972 - M. Schock, S. Schmidt, and K. Ersfeld,
Novel Cytoskeleton-Associated Proteins in Trypanosoma brucei Are Essential for Cell Morphogenesis and Cytokinesis,
Microorganisms, vol. 9, no. 11, p. 2234, 2021. doi:10.3390/microorganisms9112234
2020
- N. Ferruz, F. Lobos, D. Lemm, S. Toledo-Patino, J.A. Farías-Rico, S. Schmidt, and B. Höcker,
Identification and Analysis of Natural Building Blocks for Evolution-Guided Fragment-Based Protein Design,
Journal of Molecular Biology, vol. 432, no. 13, pp. 3898–3914, 2020. doi:10.1016/j.jmb.2020.04.013
2015
- N. Randel, R. Shahidi, C. Verasztó, L.A. Bezares-Calderón, S. Schmidt, and G. Jékely,
Inter-individual stereotypy of the Platynereis larval visual connectome,
eLife, vol. 4, p. e08069, 2015. doi:10.7554/eLife.08069 - V. Ahl, H. Keller, S. Schmidt, and O. Weichenrieder,
Retrotransposition and Crystal Structure of an Alu RNP in the Ribosome-Stalling Conformation,
Molecular Cell, vol. 60, no. 5, pp. 715–727, 2015. doi:10.1016/j.molcel.2015.10.003
2014
- J.A. Farías-Rico, S. Schmidt, and B. Höcker,
Evolutionary relationship of two ancient protein superfolds,
Nature Chemical Biology, vol. 10, no. 9, pp. 710–715, 2014. doi:10.1038/nchembio.1579
2013
- P. Bawankar, B. Loh, L. Wohlbold, S. Schmidt, and E. Izaurralde,
NOT10 and C2orf29/NOT11 form a conserved module of the CCR4-NOT complex that docks onto the NOT1 N-terminal domain,
RNA biology, vol. 10, no. 2, pp. 228–244, 2013. doi:10.4161/rna.23018 - A.M. Schneider, S. Schmidt, S. Jonas, B. Vollmer, E. Khazina, and O. Weichenrieder,
Structure and properties of the esterase from non-LTR retrotransposons suggest a role for lipids in retrotransposition,
Nucleic Acids Research, vol. 41, no. 22, pp. 10563–10572, 2013. doi:10.1093/nar/gkt786
2012
- E. Sauer, S. Schmidt, and O. Weichenrieder,
Small RNA binding to the lateral surface of Hfq hexamers and structural rearrangements upon mRNA target recognition,
Proceedings of the National Academy of Sciences of the United States of America, vol. 109, no. 24, pp. 9396–9401, 2012. doi:10.1073/pnas.1202521109 - D. Kuzuoglu-Öztürk, E. Huntzinger, S. Schmidt, and E. Izaurralde,
The Caenorhabditis elegans GW182 protein AIN-1 interacts with PAB-1 and subunits of the PAN2-PAN3 and CCR4-NOT deadenylase complexes,
Nucleic Acids Research, vol. 40, no. 12, pp. 5651–5665, 2012. doi:10.1093/nar/gks218 - A. Petit, L. Wohlbold, P. Bawankar, E. Huntzinger, S. Schmidt, E. Izaurralde, and O. Weichenrieder,
The structural basis for the interaction between the CAF1 nuclease and the NOT1 scaffold of the human CCR4-NOT deadenylase complex,
Nucleic Acids Research, vol. 40, no. 21, pp. 11058–11072, 2012. doi:10.1093/nar/gks883
2011
- E. Khazina, V. Truffault, R. Büttner, S. Schmidt, M. Coles, and O. Weichenrieder,
Trimeric structure and flexibility of the L1ORF1 protein in human L1 retrotransposition,
Nature Structural & Molecular Biology, vol. 18, no. 9, pp. 1006–1014, 2011. doi:10.1038/nsmb.2097 - A. Boland, E. Huntzinger, S. Schmidt, E. Izaurralde, and O. Weichenrieder,
Crystal structure of the MID-PIWI lobe of a eukaryotic Argonaute protein,
Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 26, pp. 10466–10471, 2011. doi:10.1073/pnas.1103946108
2010
- I.A. Adzhubei, S. Schmidt, L. Peshkin, V.E. Ramensky, A. Gerasimova, P. Bork, A.S. Kondrashov, and S.R. Sunyaev,
A method and server for predicting damaging missense mutations,
Nat Meth, vol. 7, no. 4, pp. 248–249, 2010. doi:10.1038/nmeth0410-248
2009
- N. Wittkopp, E. Huntzinger, C. Weiler, J. Saulière, S. Schmidt, M. Sonawane, and E. Izaurralde,
Nonsense-mediated mRNA decay effectors are essential for zebrafish embryonic development and survival,
Molecular and Cellular Biology, vol. 29, no. 13, pp. 3517–3528, 2009. doi:10.1128/MCB.00177-09
2008
- F. Tritschler, A. Eulalio, S. Helms, S. Schmidt, M. Coles, O. Weichenrieder, E. Izaurralde, and V. Truffault,
Similar modes of interaction enable Trailer Hitch and EDC3 to associate with DCP1 and Me31B in distinct protein complexes,
Molecular and Cellular Biology, vol. 28, no. 21, pp. 6695–6708, 2008. doi:10.1128/MCB.00759-08 - S. Schmidt, A. Gerasimova, F.A. Kondrashov, I.A. Adzhubei, I.A. Adzuhbei, A.S. Kondrashov, and S. Sunyaev,
Hypermutable non-synonymous sites are under stronger negative selection,
PLoS Genetics, vol. 4, no. 11, p. e1000281, 2008. doi:10.1371/journal.pgen.1000281 - E.A. Bennett, H. Keller, R.E. Mills, S. Schmidt, J.V. Moran, O. Weichenrieder, and S.E. Devine,
Active Alu retrotransposons in the human genome,
Genome Research, vol. 18, no. 12, pp. 1875 –1883, 2008. doi:10.1101/gr.081737.108 - K.E. Lohmueller, A.R. Indap, S. Schmidt, A.R. Boyko, R.D. Hernandez, M.J. Hubisz, J.J. Sninsky, T.J. White, S.R. Sunyaev, R. Nielsen, A.G. Clark, and C.D. Bustamante,
Proportionally more deleterious genetic variation in European than in African populations,
Nature, vol. 451, no. 7181, pp. 994–997, 2008. doi:10.1038/nature06611 - A.R. Boyko, S.H. Williamson, A.R. Indap, J.D. Degenhardt, R.D. Hernandez, K.E. Lohmueller, M.D. Adams, S. Schmidt, J.J. Sninsky, S.R. Sunyaev, T.J. White, R. Nielsen, A.G. Clark, and C.D. Bustamante,
Assessing the evolutionary impact of amino acid mutations in the human genome,
PLoS genetics, vol. 4, no. 5, p. e1000083, 2008. doi:10.1371/journal.pgen.1000083
2007
- F. Tritschler, A. Eulalio, V. Truffault, M.D. Hartmann, S. Helms, S. Schmidt, M. Coles, E. Izaurralde, and O. Weichenrieder,
A Divergent Sm Fold in EDC3 Proteins Mediates DCP1 Binding and P-Body Targeting,
Molecular and Cellular Biology, vol. 27, no. 24, pp. 8600 –8611, 2007. doi:10.1128/MCB.01506-07 - N. Ahituv, N. Kavaslar, W. Schackwitz, A. Ustaszewska, J. Martin, S. Hebert, H. Doelle, B. Ersoy, G. Kryukov, S. Schmidt, N. Yosef, E. Ruppin, R. Sharan, C. Vaisse, S. Sunyaev, R. Dent, J. Cohen, R. McPherson, and L.A. Pennacchio,
Medical sequencing at the extremes of human body mass,
American journal of human genetics, vol. 80, no. 4, pp. 779–91, 2007. - V. Spirin, S. Schmidt, A. Pertsemlidis, R.S. Cooper, J.C. Cohen, and S.R. Sunyaev,
Common Single-Nucleotide Polymorphisms Act in Concert to Affect Plasma Levels of High-Density Lipoprotein Cholesterol,
Am J Hum Genet, vol. 81, no. 6, 2007.
2006
- S. Savas, S. Schmidt, H. Jarjanazi, and H. Ozcelik,
Functional nsSNPs from carcinogenesis-related genes expressed in breast tissue: potential breast cancer risk alleles and their distribution across human populations,
Human Genomics, vol. 2, no. 5, pp. 287–296, 2006. doi:10.1186/1479-7364-2-5-287
2005
- G.V. Kryukov, S. Schmidt, and S. Sunyaev,
Small fitness effect of mutations in highly conserved non-coding regions,
Human molecular genetics, vol. 14, no. 15, pp. 2221–9, 2005. - T. Dandekar and S. Schmidt,
Metabolites and pathway flexibility,
In silico biology, vol. 5, no. 2, pp. 103–10, 2005. [Online]. Available: http://www.bioinfo.de/isb/2004050012/ - S. Asthana, S. Schmidt, and S. Sunyaev,
A limited role for balancing selection,
Trends in genetics: TIG, vol. 21, no. 1, pp. 30–32, 2005. doi:10.1016/j.tig.2004.11.001 - M.F. Rudd, R.D. Williams, E.L. Webb, S. Schmidt, G.S. Sellick, and R.S. Houlston,
The predicted impact of coding single nucleotide polymorphisms database,
Cancer Epidemiology, Biomarkers & Prevention: A Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology, vol. 14, no. 11 Pt 1, pp. 2598–2604, 2005. doi:10.1158/1055-9965.EPI-05-0469
2004
- I. Letunic, R. Copley, S. Schmidt, F. Ciccarelli, T. Doerks, J. Schultz, C. Ponting, and P. Bork,
SMART 4.0: towards genomic data integration,
Nucleic acids research, vol. 32, no. Database issue, pp. D142–4, 2004. doi:10.1093/nar/gkh088 - J.E. Morett-Sanchez, L. Olvera-Rodriguez, M. Olvera-Rodriguez, E.R. Mani, G. Saab-Rincon, P. Bork, D. Korbelarz, S. Schmidt, and D.H.P. Snel, Bioinformatic method for predicting functional equivalence between biological sequences, 2004. [Online]. Available: https://patents.google.com/patent/WO2004099404A2/en [Accessed: Dec. 15, 2021].
- M. Dünßer, R. Lampidis, S. Schmidt, D. Seipel, and T. Dandekar,
Integration of Data in Pathogenomics: Three Layers of cellular complexity and an XML-based Framework,
Journal of Integrative Bioinformatics, vol. 1, no. 1, pp. 52–63, 2004. doi:10.1515/jib-2004-5
2003
- S. Schmidt, S. Sunyaev, P. Bork, and T. Dandekar,
Metabolites: a helping hand for pathway evolution?,
Trends in biochemical sciences, vol. 28, no. 6, pp. 336–41, 2003. [Online]. Available: http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TCV-48TMGM6-1&_user=29041&_coverDate=06%252F30%252F2003&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000003178&_version=1&_urlVersion=0&_userid=29041&md5=29d0a750fc2da98ad8d70ad3358dd49a - E. Morett, J. Korbel, E. Rajan, G. Saab-Rincon, L. Olvera, M. Olvera, S. Schmidt, B. Snel, and P. Bork,
Systematic discovery of analogous enzymes in thiamin biosynthesis,
Nature biotechnology, vol. 21, no. 7, pp. 790–5, 2003. doi:10.1038/nbt834 - C. Mering, M. Huynen, D. Jaeggi, S. Schmidt, P. Bork, and B. Snel,
STRING: a database of predicted functional associations between proteins,
Nucleic Acids Research, vol. 31, no. 1, pp. 258–261, 2003. doi:10.1093/nar/gkg034
2002
- S. Schmidt, P. Bork, and T. Dandekar,
A versatile structural domain analysis server using profile weight matrices,
Journal of chemical information and computer sciences, vol. 42, no. 2, pp. 405–7, 2002. [Online]. Available: http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/ci010374r - T. Dandekar, B. Snel, S. Schmidt, W. Lathe, M. Suyama, M. Huynen, and P. Bork,
Comparative Genome Analysis of the Mollicutes,
in Molecular Biology and Pathogenicity of Mycoplasmas, S. Razin and R. Herrmann, Eds. Boston, MA: Springer US, 2002, pp. 255–278.doi:10.1007/0-306-47606-1_11 - S. Schmidt and T. Dandekar,
Metabolic Pathways,
In Proc. Gene Regulations and Metabolism - Postgenomic Computational Approaches, 2002, p. 251–272. - E. Morett, J. Korbel, K. Emmanuvel Rajan, G. Saab Rincon, L. Olvera, M. Olvera, S. Schmidt, B. Snel, and P. Bork,
Discovery of Analogous Enzymes in Thiamin Biosynthesis by Anticorrelation,
Genome Informatics, vol. 13, 2002. - B. Höcker, S. Schmidt, and R. Sterner,
A common evolutionary origin of two elementary enzyme folds,
FEBS letters, vol. 510, no. 3, pp. 133–135, 2002. doi:10.1016/s0014-5793(01)03232-x - M. Henn-Sax, R. Thoma, S. Schmidt, M. Hennig, K. Kirschner, and R. Sterner,
Two (betaalpha)(8)-barrel enzymes of histidine and tryptophan biosynthesis have similar reaction mechanisms and common strategies for protecting their labile substrates,
Biochemistry, vol. 41, no. 40, pp. 12032–12042, 2002. doi:10.1021/bi026092h
2001
- T. Dandekar, F. Du, R. Schirmer, and S. Schmidt,
Medical target prediction from genome sequence: combining different sequence analysis algorithms with expert knowledge and input from artificial intelligence approaches,
Computers & chemistry, vol. 26, no. 1, pp. 15–21, 2001. [Online]. Available: http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TFV-44BD48D-3&_user=29041&_coverDate=12%252F31%252F2001&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000003178&_version=1&_urlVersion=0&_userid=29041&md5=469ec5702907380456dbe964a2cd7578
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