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Höcker lab – Protein Design

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Publications

2022

Ferruz N., Schmidt S., Höcker B. (2022) ProtGPT2 is a deep unsupervised language model for protein design Nat Commun doi: 10.1038/s41467-022-32007-7 [PubMed]

Rhys G.G., Cross J.A., Dawson W.M, Thompson H.F., Shanmugaratnam S., Savery N.J., Dodding M.P., Höcker B., Woolfson D.N. (2022) De novo designed peptides for cellular delivery and subcellular localisation Nat Chem Biol doi: 10.1038/s41589-022-01076-6 [PubMed]

Ferruz N., Höcker B. (2022) Controllable protein design with language models Nat Mach Intell doi: 10.1038/s42256-022-00499-z [PubMed]

Kynast J.P., Schwägerl F., Höcker B. (2022) ATLIGATOR: Editing protein interactions with an atlas-based approach bioRxiv doi:  [BioRxiv]

Gisdon J.F., Kynast J.P., Ayyildiz M., Hine A.V., Plückthun A., Höcker B. (2022) Modular peptide binders - development of a predective technology as alternative for reagent antibodies Biol Chem doi: 10.1515/hsz-2021-0384 [PubMed]

Ferruz N., Höcker B. (2022) Dreaming ideal protein structures Nat Biotechnol doi: 10.1038/s41587-021-01196-9 [PubMed]

2021

Kordes S., Romero-Romero S., Lutz L, Höcker B. (2021) A newly introduced salt bridge cluster improves structural and biophysical properties of de novo TIM barrels Prot Sci doi: 10.1002/pro.4249 [PubMed]

Kröger P., Shanmugaratnam S., Scheib U., Höcker B. (2021) Fine-tuning spermidine binding modes in the putrescine binding protein PotF J Biol Chem doi: 10.1016/j.jbc.2021.101419 [PubMed]

Menzel T., Weigert S., Gagsteiger A., Eich Y., Sittl S., Papastavrou G., Ruckdäschel H., Altstädt V., Höcker B. (2021) Impact of Enzymatic Degradation on the Material Properties of Poly(Ethylene Terephthalate) Polymers doi: 10.3390/polym13223885 [PubMed]

Ferruz N., Michel F., Lobos F., Schmidt S., Höcker B. (2021) Fuzzle 2.0: Ligand Binding in Natural Protein Building Blocks Front Mol Biosci doi: 10.3389/fmolb.2021.715972 [PubMed]

Weigert S., Gagsteiger A., Menzel T., Höcker B. (2021) A versatile assay platform for enzymatic poly(ethylene-terephthalate) degradation Protein Eng Des Sel doi: 10.1093/protein/gzab022 [PubMed]

Reichert D., Schepers H., Simke J., Lechner H., Dörner W., Höcker B., Ravoo BJ, Rentmeister A (2021) Computational design and experimental characterization of a photo-controlled mRNA-cap guanine-N7 methyltransferase RSC Chem Biol doi: 10.1039/D1CB00109D [PubMed]

Romero-Romero S., Costas M., Silva Manzano D.A., Kordes S., Rojas-Ortega E., Tapia C., Guerra Y., Shanmugaratnam S., Rodríguez-Romero A., Baker D., Höcker B., Fernández-Velasco D.A. (2021) The Stability Landscape of de novo TIM Barrels Explored by a Modular Design Approach J Mol Biol doi: 10.1016/j.jmb.2021.167153 [PubMed]

Ferruz N., Schmidt S., Höcker B. (2021) ProteinTools: a toolkit to analyze protein structures Nucleic Acids Res doi: 10.1093/nar/gkab375 [PubMed]

Ferruz N., Noske J., Höcker B. (2021) Protlego: A Python package for the analysis and design of chimeric proteins Bioinformatics doi: 10.1093/bioinformatics/btab253 [PubMed]

Herud-Sikimic, Stiel A.C., Kolb M., Shanmugaratnam S., Berendzen K.W., Feldhaus C., Höcker B., Jürgens G. (2021) A biosensor for the direct visualization of auxin Nature doi: 10.1038/s41586-021-03425-2 [PubMed]

Wiese J.G., Shanmugaratnam S., Höcker B. (2021) Extension of a de novo TIM barrel with a rationally designed secondary structure element Prot Sci doi: 10.1002/pro.4064 [PubMed]

Romero-Romero S., Kordes S., Michel F., Höcker B. (2021) Evolution, folding, and design of TIM barrels and related proteins Curr Opin Struct Biol doi: 10.1016/j.sbi.2020.12.007 [PubMed]

Lechner H., Emann R. V., Breuning M., Höcker B. (2021) An Artificial Cofactor Catalyzing the Baylis-Hillman Reaction using Designed Streptavidin as Protein Host Chembiochem doi: 10.1002/cbic.202000880 [PubMed]

2020

Kröger P., Shanmugaratnam S., Ferruz N., Schweimer K., Höcker B. (2020) A comprehensive binding study illustrates ligand recognition in the periplasmic binding protein PotF Structure doi: 10.1016/j.str.2020.12.005 [PubMed]

Stiel A.C., Shanmugaratnam S., Herud-Sikimic O., Jürgens G., Höcker B. (2020) Ligand promiscuity in the tryptophan repressor – from structural understanding towards rational design BioRxiv doi: 10.1101/2020.01.20.912972 [BioRxiv]

Linke H., Höcker B., Furuta K., Forde N.C., Curmi P.M.G. (2020) Synthetic biology approaches to dissecting linear motor protein function: towards the design and synthesis of artificial autonomous protein walkers. Biophys Rev doi: 10.1007/s12551-020-00717-1 [PubMed]

Ferruz N., Lobos F., Lemm D., Toledo-Patino S., Arcadio Farías-Rico J., Schmidt S., Höcker B., (2020) Identification and Analysis of Natural Building Blocks for Evolution-Guided Fragment-Based Protein Design J Mol Biol, doi: 10.1016/j.jmb.2020.04.013 [PubMed]

2019

Toledo Patino S., Chaubey M., Coles M., Höcker B., (2019) Reconstructing the remote origins of a fold singleton from a flavodoxin-like ancestor Biochemistry, doi: 10.1021/acs.biochem.9b00900 [PubMed]

2018

Lechner, H., Ferruz N., Höcker B., (2018) Strategies for designing non-natural enzymes and binders. Curr Opin Chem Biol 47:67-76, doi: 10.1016/j.cbpa.2018.07.022 [PubMed]

Lichtenstein, B. R., Höcker, B. (2018) Engineering an AB5 Protein Carrier. Sci Rep doi: 10.1038/s41598-018-30910-y [PubMed]

Banda-Vázquez, J., Shanmugaratnam, S., Rodríguez-Sotres, R., Torres-Larios, A., Höcker, B. & Sosa-Peinado, A. (2018) Redesign of LAOBP to bind novel L-amino acid ligands. Protein Sci doi: 10.1002/pro.3403. [PubMed]

Höcker, B. & Winther, J.R. (2018) Editorial Overview: A perspective on protein evolution. Curr Opin Struc Biol 48, viii-ix. [PubMed] - Editorial to the February issue on "Proteins" edited by Jakob & myself

2017

Toledo-Patino, S., Lobos, F. & Höcker, B. (2017) Baukasten der Natur: Neue Proteine aus konservierten Fragmenten. BIOspektrum 23(6), 630-633. [BIOspektrum]

Sterner, R., Höcker, B. & Kolmar, H. (2017) Highlight issue: Protein Design. Biol Chem 398, 1-2. [PubMed]

2016

Stiel, A., Nellen, M. & Höcker, B. (2016) PocketOptimizer and the design of ligand binding sites. Methods Mol Biol 1414:63-75. [PubMed]

Huang, P.-S.*, Feldmeier, K.*, Parmeggiani, F., Fernandez Velasco, D.A., Höcker, B. & Baker, D. (2016) De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy. Nature Chem Biol 12:29-34. [PubMed]

2014

Stiel, A., Feldmeier, K. & Höcker, B. (2014) Identification of protein scaffolds for enzyme design using ScaffoldSelection. Methods Mol Biol 1216:183-96. [PubMed]
 
Farias-Rico, J.A., Schmidt, S. & Höcker, B. (2014) Evolutionary relationship of two ancient protein superfolds. Nature Chem Biol 10:710-5. [PubMed]
 
Höcker, B. (2014) Design of proteins from smaller fragments - learning from evolution. Curr Opin Struc Biol 27:56-62. [PubMed]
 
Höcker, B. & Midelfort, K. (2014) Editorial: Designing protein function - Macromolecular design. J Struc Biol 185:135. [PubMed] - Editorial to the special issue on "Macromolecular Design" edited by Katarina & myself
 
Scheib, U., Shanmugaratnam, S., Farias-Rico, J.A. & Höcker, B. (2014) Change in protein-ligand specificity through binding pocket grafting. J Struc Biol 185:186-92. doi: 10.1016/j.jsb.2013.06.002. Epub 2013 Jun17. [PubMed]

2013


Feldmeier, K. & Höcker, B. (2013) Computational protein design of ligand binding and catalysis. Curr Opin Chem Biol 17:929–933.[PubMed]
 
Höcker, B. (2013) Engineering chimaeric proteins from fold fragments: 'hopeful monsters' in protein design. Biochem Soc Trans 41:1137-40. [PubMed]
 
Meier, M.M.,Rajendran, C., Malisi, C., Fox, N.G., Xu, C., Schlee, S., Barondeau, D.P., Höcker, B., Sterner, R. & Raushel, F.M. (2013) Molecular Engineering of organophosphate hydrolysis activity from a weak promiscuous lactonase template. J Am Chem Soc 135, 11670-7. [PubMed]
 
Farias-Rico, J.A. & Höcker, B. (2013) Design of chimeric proteins by combination of subdomain-sized fragments. Methods Enzymol 523, 389-405. [PubMed]

2012

Malisi, C., Schumann, M., Toussaint, N.C., Kageyama, J., Kohlbacher, O. & Höcker, B. (2012) Binding pocket optimization by computational protein design.
PLoS One 7(12):e52505. [PubMed]
 
Höcker, B. (2012) A toolbox for protein design. Nature 491, 204-5. [PubMed]
News & Views on Koga et al. (2012): Principles for designing ideal protein structures.
 
Shanmugaratnam, S., Eisenbeis, S. & Höcker, B. (2012) A highly stable protein chimera built from fragments of different folds. Protein Eng Des Sel 25, 699-703. [PubMed]
 
Höcker, B. (2012) A metalloenzyme reloaded. Nature Chem Biol 8, 224-5. [PubMed]
News & Views on Khare et al. (2012): Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis.
 
Eisenbeis, S., Proffitt, W., Coles, M., Truffault, V., Shanmugaratnam, S., Meiler, J. & Höcker, B. (2012) The potential of fragment recombination for the rational design of proteins. 
J Am Chem Soc 134, 4019-22. [PubMed

2011


Höcker, B. Einblicke in die Mechanismen der Evolution durch Protein Design. Jahrbuch der Akademie der Wissenschaften zu Göttingen 2011, S. 183-187, De Gruyter.
 
Malisi, C., Stiel, A.C. & Höcker, B. (2011) Enzyme am Reißbrett. BIOspektrum 17(7), 736-8. [BIOspektrum]

2010


Höcker, B. (2010) Mechanismen der Evolution als Matrize für Protein Engineering. (Forschungsbericht 2010 - MPI für Entwicklungsbiologie).
 
Schreier, B. & Höcker, B. (2010) Engineering the enolase magnesium II bindding site: implications for its evolution. Biochemistry 49, 7582-9. [PubMed]
 
Eisenbeis, S. & Höcker, B. (2010) Evolutionary mechanism as a template for protein engineering. J Pep Sci 16, 538-44. [PubMed]
 
Höcker, B. (2010) Metals make proteins stick. Chem Biol 17, 103-4. [PubMed]
Preview on Salgado et al. (2010): Metal templated design of protein interfaces.

2009


Schreier, B., Stumpp, C., Wiesner, S. & Höcker, B. (2009) Computational design of ligand binding is not a solved problem. Proc Natl Acad Sci 106, 18491-6. [PubMed]   
Media coverage in Nature News & in The Scientist  
 
Malisi, C., Kohlbacher, O. & Höcker, B. (2009) Automated scaffold selection for enzyme design. Proteins 77, 74-83. [PubMed]
 
Claren, J., Malisi, C., Höcker, B. & Sterner, R. (2009) Establishing wild-type levels of catalytic activity on natural and artificial (βα)8-barrel protein scaffolds.
Proc Natl Acad Sci 106, 3704-9. [PubMed]  
 
Höcker, B., Lochner, A., Seitz, T., Claren, J. & Sterner, R. (2009) High-resolution crystal structure of an artificial (βα)8-barrel protein designed from identical half-barrels. Biochemistry 48, 1145-1147. [PubMed]

2008


Höcker, B. Chapter 8: Structural frameworks suitable for engineering. In Protein Engineering Handbook. Eds. S.Lutz & U.T.Bornscheuer. Wiley-VCH 2008.
 
Bharat, T.A.M., Eisenbeis, S., Zeth, K. & Höcker, B. (2008) A βα-barrel built by the combination of fragments from different folds. 
Proc Natl Acad Sci 105, 9942-7. [PubMed]  
 
Höcker, B. (2008). Proteindesign und -engineering. Trendbericht in Biochemie und Molekularbiologie. Nachrichten aus der Chemie 56/3, 298-301. [GDCh]


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