Publications
Protein Evolution

Journal Article (411)

1.
Journal Article
Grandchamp, A.; Czuppon, P.; Bornberg-Bauer, E.: Quantification and modeling of turnover dynamics of de novo transcripts in Drosophila melanogaster. Nucleic Acids Research 52 (1), pp. 274 - 287 (2024)
2.
Journal Article
Hartmann, M.: TRIM for Tissue Specificity. ACS Medicinal Chemistry Letters 15 (1), pp. 4 - 5 (2024)
3.
Journal Article
Winski, A.; Ludwiczak, J.; Orlowska, M.; Madaj, R.; Kaminski, K.; Dunin-Horkawicz, S.: AlphaFold2 captures the conformational landscape of the HAMP signaling domain. Protein Science 33 (1), e4846 (2024)
4.
Journal Article
Alexander, L.; Durairaj, J.; Kryshtafovych, A.; Abriata, L.; Bayo, Y.; Bhabha, G.; Breyton, C.; Caulton, S.; Chen, J.; Degroux, S. et al.; Ekiert, D.; Erlandsen, B.; Freddolino, P.; Gilzer, D.; Greening, C.; Grimes, J.; Grinter, R.; Gurusaran, M.; Hartmann, M.; Hitchman, C.; Keown, J.; Kropp, A.; Kursula, P.; Lovering, A.; Lemaitre, B.; Lia, A.; Liu, S.; Logotheti, M.; Lu, S.; Markússon, S.; Miller, M.; Minasov, G.; Niemann, H.; Opazo, F.; Phillips jr, G.; Davies, O.; Rommelaere, S.; Rosas-Lemus, M.; Roversi, P.; Satchell, K.; Smith, N.; Wilson, M.; Wu, K.-L.; Xia, X.; Xiao, H.; Zhang, W.; Zhou, Z.; Fidelis, K.; Topf, M.; Moult, J.; Schwede, T.: Protein target highlights in CASP15: Analysis of models by structure providers. Proteins: Structure, Function, and Bioinformatics 91 (12), pp. 1571 - 1599 (2023)
5.
Journal Article
Bharat, T.; Tocheva, E.; Alva, V.: The cell envelope architecture of Deinococcus: HPI forms the S-layer and SlpA tethers the outer membrane to peptidoglycan. Proceedings of the National Academy of Sciences of the United States of America 120 (51), e2305338120 (2023)
6.
Journal Article
Joiner, J.; Steinchen, W.; Mozer, N.; Kronenberger, T.; Bange, G.; Poso, A.; Wagner, S.; Hartmann, M.: HilE represses the activity of the Salmonella virulence regulator HilD via a mechanism distinct from that of intestinal long-chain fatty acids. The Journal of Biological Chemistry 299 (12), 105387 (2023)
7.
Journal Article
Fonseca Lopez, F.; Miao, J.; Damjanovic, J.; Bischof, L.; Braun, M.; Ling, Y.; Hartmann, M.; Lin, Y.-S.; Kritzer, J.: Computational Prediction of Cyclic Peptide Structural Ensembles and Application to the Design of Keap1 Binders. Journal of Chemical Information and Modeling 63 (21), pp. 6925 - 6937 (2023)
8.
Journal Article
Smug, B.; Szczepaniak, K.; Riocha, E.; Dunin-Horkawicz, S.; Mostowy, R.: Ongoing shuffling of protein fragments diversifies core viral functions linked to interactions with bacterial hosts. Nature Communications 14 (1), 7460 (2023)
9.
Journal Article
Steinebach, C.; Bricelj, A.; Murgai, A.; Sosič, I.; Bischof, L.; Ng, Y.; Heim, C.; Maiwald, S.; Proj, M.; Voget, R. et al.; Feller, F.; Košmrlj, J.; Sapozhnikova, V.; Schmidt, A.; Zuleeg, M.; Lemnitzer, P.; Mertins, P.; Hansen, F.; Gütschow, M.; Krönke, J.; Hartmann, M.: Leveraging Ligand Affinity and Properties: Discovery of Novel Benzamide-Type Cereblon Binders for the Design of PROTACs. Current Medicinal Chemistry 66 (21), pp. 14513 - 14543 (2023)
10.
Journal Article
Aubel, M.; Eicholt, L.; Bornberg-Bauer, E.; Lange, A.: Wie de novo entstandene Proteine im Labor exprimiert werden können. Biospektrum 29 (6), pp. 629 - 632 (2023)
11.
Journal Article
Kaminski, K.; Ludwiczak, J.; Pawlicki, K.; Alva, V.; Dunin-Horkawicz, S.: pLM-BLAST: distant homology detection based on direct comparison of sequence representations from protein language models. Bioinformatics 39 (10), btad579 (2023)
12.
Journal Article
Zibat, A.; Zhang, X.; Dickmanns, A.; Stegmann, K.; Dobbelstein, A.; Alachram, H.; Soliwoda, R.; Salinas, G.; Görlich, D.; Kschischo, M. et al.; Wollnik, B.; Dobbelstein, M.: N4-hydroxycytidine, the active compound of Molnupiravir, promotes SARS-CoV-2 mutagenesis and escape from a neutralizing nanobody. iScience 26 (10), 107786 (2023)
13.
Journal Article
Fouks, B.; Harrison, M.; Mikhailova, A.; Marchal, E.; English, S.; Carruthers, M.; Jennings, E.; Pippel, M.; Attardo, G.; Benoit, B. et al.; Bornberg-Bauer, E.; Tobe, S.: Live-bearing cockroach genome reveals convergent evolutionary mechanisms linked to viviparity in insects and beyond. iScience 26 (10), 107832 (2023)
14.
Journal Article
Martinez-Goikoetxea, M.; Lupas, A.: New protein families with hendecad coiled coils in the proteome of life. Journal of Structural Biology 215 (3), 108007 (2023)
15.
Journal Article
Maksymenko, K.; Maurer, A.; Aghaallaei, N.; Barry, C.; Borbarán-Bravo, N.; Ullrich, T.; Dijkstra, T.; Hernandez-Alvarez, B.; Müller, P.; Lupas, A. et al.; Skokowa, J.; ElGamacy, M.: The design of functional proteins using tensorized energy calculations. Cell Reports Methods 3 (8), 100560 (2023)
16.
Journal Article
Podobnik, M.; Singh, A.; Fu, Z.; Dooley, C.; Frohnhöfer, H.; Firlej, M.; Stednitz, S.; Elhabashy, H.; Weyand, S.; Weir, J. et al.; Lu, J.; Nüsslein-Volhard, C.; Irion, U.: kcnj13 regulates pigment cell shapes in zebrafish and has diverged by cis-regulatory evolution between Danio species. Development 150 (16), dev.201627 (2023)
17.
Journal Article
Wu, Y.; Chen, K.-W.; Li, Y.-N.; Qiu, K.-Y.; Lu, G.; Shu, T.; Sun, T.-Y.; Hou , Z.-Q.; Wu, Y.-D.; Yu, L.-J.: Propeptide-Mediated Allosteric Regulation of Xylanase Xyl-1: An Integrated Experimental and Computational Analysis. Journal of Agricultural and Food Chemistry 71 (30), pp. 11692 - 11703 (2023)
18.
Journal Article
Braun, V.; Ratcliff, A.; Celia, H.; Buchanan, S.: Energization of Outer Membrane Transport by the ExbB ExbD Molecular Motor. Journal of Bacteriology 205 (6), e0003523 (2023)
19.
Journal Article
Grandchamp, A.; Kühl, L.; Lebherz, M.; Brüggemann, K.; Parsch, J.; Bornberg-Bauer, E.: Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster. Genome Research 33 (6), pp. 872 - 890 (2023)
20.
Journal Article
Fuchs, A.: Specific, sensitive and quantitative protein detection by in-gel fluorescence. Nature Communications 14 (1), 2505 (2023)
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