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RESEARCH PAPER · ChemBioChem · 2016

BioCatNet: A Database System for the Integration of Enzyme Sequences and Biocatalytic Experiments

Patrick C. F. Buchholz, Constantin Vogel, Waldemar Reusch, Martina Pohl, Dörte Rother, Antje C. Spieß, Jürgen Pleiss

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BioCatNet: A Database System for the Integration of Enzyme Sequences and Biocatalytic ExperimentsOriginalMining the Arabidopsis genome for cytochrome P450 biocatalysts0Biocatalytic study of novel oleate hydratases49Harnessing plant metabolic diversity80Protein engineering of enzymes involved in lipid modification3The ω‐transaminase engineering database (oTAED): A navigation tool in protein sequence and structure space26Interpretation of cytochrome P450 monooxygenase kinetics by modeling of thermodynamic activity8STRENDA DB: enabling the validation and sharing of enzyme kinetics data64Towards a Mechanistic Understanding of Factors Controlling the Stereoselectivity of Transketolase1Progress Curve Analysis Within BioCatNet: Comparing Kinetic Models for Enzyme-Catalyzed Self-Ligation11Structural and Mutagenesis Studies of the Thiamine‐Dependent, Ketone‐Accepting YerE from Pseudomonas protegens19Biodegradation of Pesticides in Brazil and Other Tropical Countries: Experimental and In Silico Studies2The Short‐chain Dehydrogenase/Reductase Engineering Database (SDRED): A classification and analysis system for a highly diverse enzyme family50A simple linearization method unveils hidden enzymatic assay interferences9The modular structure of α/β‐hydrolases138Advances in biological conversion technologies: new opportunities for reaction engineering26Simulation Foundry: Automated and F.A.I.R. Molecular Modeling14Multicopper oxidases: modular structure, sequence space, and evolutionary relationships55Expansin Engineering Database: A navigation and classification tool for expansins and homologues29Assessing the Thiamine Diphosphate Dependent Pyruvate Dehydrogenase E1 Subunit for Carboligation Reactions with Aliphatic Ketoacids12Endolysins from Antarctic Pseudomonas Display Lysozyme Activity at Low Temperature20Rocker Models for Reliable Detection and Typing of Short Read Sequences Carrying β-lactamases2Enzyme Cascade Design: Retrosynthesis Approach5Biocatalysis685Modeling‐Assisted Design of Thermostable Benzaldehyde Lyases from Rhodococcus erythropolis for Continuous Production of α‐Hydroxy Ketones16The GH19 Engineering Database: Sequence diversity, substrate scope, and evolution in glycoside hydrolase family 1948eScience Infrastructures in Physical Chemistry3ROCker Models for Reliable Detection and Typing of Short-Read Sequences Carrying β-Lactamase Genes6Machine learning-enabled retrobiosynthesis of molecules120A Novel Pathway for Biosynthesis of the Herbicidal Phosphonate Natural Product Phosphonothrixin Is Widespread in Actinobacteria11Binding Interactions and Inhibition Mechanisms of Gold Complexes in Thiamine Diphosphate-Dependent Enzymes4Enzyme Databases in the Era of Omics and Artificial Intelligence31Recent trends in biocatalysis and its application in the food industry2Genome sequencing and molecular networking analysis of the wild fungus Anthostomella pinea reveal its ability to produce a diverse range of secondary metabolites11FAIR Data and Software: Improving Efficiency and Quality of Biocatalytic Science13Latest Trends in Lipase-Catalyzed Synthesis of Ester Carbohydrate Surfactants: From Key Parameters to Opportunities and Future Development30Identification and Characterization of Thiamine Diphosphate‐Dependent Lyases with an Unusual CDG Motif9Identification and Characterization of Thiamine Diphosphate‐Dependent Lyases with an Unusual CDG Motif0Identification of Kibdelomycin and Related Biosynthetic Gene Clusters and Characterization of the C‐Branching of Amycolose5Identification of Kibdelomycin and Related Biosynthetic Gene Clusters and Characterization of the C‐Branching of Amycolose1Digitalization of biocatalysis: Best practices to research data management2Data-driven revolution of enzyme catalysis from the perspective of reactions, pathways, and enzymes7Independent evolution of betulin biosynthesis in Inonotus obliquus2zERExtractor: An Automated Platform for Enzyme-Catalyzed Reaction Data Extraction from Scientific Literature3A motif-based deep learning tool for the identification of unusual NADH-dependent imine reductases4Mechanistic insights into activity-enhancing mutations from comparative analysis of two Bacillus subtilis GH11 xylanases0Applications and limitations of AI tools in enzyme design1Thiamine Diphosphate‐Dependent Biocatalysis in the 21 st Century0

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  1. Mining the Arabidopsis genome for cytochrome P450 biocatalysts

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    Maria Magdalena Razalan

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  2. Biocatalytic study of novel oleate hydratases

    Journal of Molecular Catalysis B Enzymatic · 2016-11-01

    Jens Schmid, Lisa Steiner, Silvia Fademrecht, Jürgen Pleiss, Konrad B. Otte, Bernhard Hauer

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  3. Harnessing plant metabolic diversity

    Current Opinion in Chemical Biology · 2017-05-17

    Charlie Owen, Nicola J. Patron, Ancheng C. Huang, Anne Osbourn

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  4. Protein engineering of enzymes involved in lipid modification

    Elsevier eBooks · 2018-01-01

    Isabel Oroz‐Guinea, Katja Zorn, Henrike B. Brundiek

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  5. The ω‐transaminase engineering database (oTAED): A navigation tool in protein sequence and structure space

    Proteins Structure Function and Bioinformatics · 2018-02-09

    Oliver Buß, Patrick C. F. Buchholz, Maike Gräff, Peter Klausmann, Jens Rudat, Jürgen Pleiss

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  6. Interpretation of cytochrome P450 monooxygenase kinetics by modeling of thermodynamic activity

    Journal of Inorganic Biochemistry · 2018-03-02

    Valerio Ferrario, Niels Hansen, Jürgen Pleiss

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  7. STRENDA DB: enabling the validation and sharing of enzyme kinetics data

    FEBS Journal · 2018-03-02

    Neil Swainston, Antonio Baici, Barbara M. Bakker, Athel J. Cornish-Bowden, Paul F. Fitzpatrick, Peter J. Halling, Thomas S. Leyh, Claire O’Donovan, Frank M. Raushel, Udo Reschel, Johann M. Rohwer, Santiago D. Schnell, Dietmar Schomburg, Keith Francis Tipton, Ming‐Daw Tsai, Hans Victor Westerhoff, Ulrike Wittig, Roland Wohlgemuth, Carsten Kettner

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  8. Towards a Mechanistic Understanding of Factors Controlling the Stereoselectivity of Transketolase

    ChemCatChem · 2018-03-23

    Anna Baierl, Axel Theorell, Ursula Mackfeld, Philipp Marquardt, Friederike Hoffmann, Stephanie Moers, Katharina Nöh, Patrick C. F. Buchholz, Jürgen Pleiss, Martina Pohl

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  9. Progress Curve Analysis Within BioCatNet: Comparing Kinetic Models for Enzyme-Catalyzed Self-Ligation

    Biotechnology Journal · 2018-07-12

    Patrick C. F. Buchholz, Rüdiger Ohs, Antje C. Spieß, Jürgen Pleiss

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  10. Structural and Mutagenesis Studies of the Thiamine‐Dependent, Ketone‐Accepting YerE from Pseudomonas protegens

    ChemBioChem · 2018-08-13

    Sabrina Hampel, Jan‐Patrick Steitz, Anna Baierl, Patrizia Lehwald, Luzia Wiesli, Michael Richter, Alexander Fries, Martina Pohl, Gunter Schneider, Doreen Dobritzsch, Michael Müller

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  11. Biodegradation of Pesticides in Brazil and Other Tropical Countries: Experimental and In Silico Studies

    Microorganisms for sustainability · 2019-01-01

    Maricy Raquel Lindenbah Bonfá, Rodrigo Matheus Pereira, Rômulo Penna Scorza Júnior, Caio César Achiles do Prado

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  12. The Short‐chain Dehydrogenase/Reductase Engineering Database (SDRED): A classification and analysis system for a highly diverse enzyme family

    Proteins Structure Function and Bioinformatics · 2019-02-04

    Maike Gräff, Patrick C. F. Buchholz, Peter Stockinger, Bettina Bommarius, Andreas Sebastian Bommarius, Jürgen Pleiss

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  13. A simple linearization method unveils hidden enzymatic assay interferences

    Biophysical Chemistry · 2019-05-28

    Maria Filipa Pinto, Jorge Ripoll‐Rozada, Helena Ramos, Emma E. Watson, Charlotte Franck, Richard J. Payne, Lucı́lia Saraiva, Pedro José Barbosa Pereira, Annalisa Pastore, Fernando A. Rocha, Pedro Miguel Martins

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  14. The modular structure of α/β‐hydrolases

    FEBS Journal · 2019-09-23

    Tabea L. Bauer, Patrick C. F. Buchholz, Jürgen Pleiss

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  15. Advances in biological conversion technologies: new opportunities for reaction engineering

    Reaction Chemistry & Engineering · 2020-01-01

    John M. Woodley

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  16. Simulation Foundry: Automated and F.A.I.R. Molecular Modeling

    Journal of Chemical Information and Modeling · 2020-04-02

    Gudrun Gygli, Juergen Pleiss

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  17. Multicopper oxidases: modular structure, sequence space, and evolutionary relationships

    Proteins Structure Function and Bioinformatics · 2020-05-24

    Maike Gräff, Patrick C. F. Buchholz, Marilize Le Roes‐Hill, Jürgen Pleiss

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  18. Expansin Engineering Database: A navigation and classification tool for expansins and homologues

    Proteins Structure Function and Bioinformatics · 2020-08-30

    Caroline Lohoff, Patrick C. F. Buchholz, Marilize Le Roes‐Hill, Jürgen Pleiss

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  19. Assessing the Thiamine Diphosphate Dependent Pyruvate Dehydrogenase E1 Subunit for Carboligation Reactions with Aliphatic Ketoacids

    International Journal of Molecular Sciences · 2020-11-16

    Stefan R. Marsden, Duncan G. G. McMillan, Ulf Hanefeld

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  20. Endolysins from Antarctic Pseudomonas Display Lysozyme Activity at Low Temperature

    Marine Drugs · 2020-11-20

    Marco Orlando, Sandra Pucciarelli, Marina Lotti

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  21. Rocker Models for Reliable Detection and Typing of Short Read Sequences Carrying β-lactamases

    Research Square · 2020-11-25

    Siyu Zhang, Brittany Suttner, Luis M. Rodriguez‐R, Luis H. Orellana, Jessica Lauren Rowell, Hattie E. Webb, Amanda Williams, Andrew Huang, Konstantinos T. Konstantinidis

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  22. Enzyme Cascade Design: Retrosynthesis Approach

    Springer eBooks · 2021-01-01

    William Finnigan, Sabine Lahja Flitsch, Lorna J. Hepworth, Nicholas John Turner

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  23. Biocatalysis

    Nature Reviews Methods Primers · 2021-06-24

    Elizabeth L. Bell, William Finnigan, Scott P. France, Anthony P. Green, Martin A. Hayes, Lorna J. Hepworth, Sarah L. Lovelock, Haruka Niikura, Sílvia Osuna, Elvira Romero, Katherine S. Ryan, Nicholas John Turner, Sabine Lahja Flitsch

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  24. Modeling‐Assisted Design of Thermostable Benzaldehyde Lyases from Rhodococcus erythropolis for Continuous Production of α‐Hydroxy Ketones

    ChemBioChem · 2021-09-24

    Martin Peng, Dominik L. Siebert, Martin K. M. Engqvist, Christof M. Niemeyer, Kersten S. Rabe

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  25. The GH19 Engineering Database: Sequence diversity, substrate scope, and evolution in glycoside hydrolase family 19

    PLoS ONE · 2021-10-26

    Marco Orlando, Patrick C. F. Buchholz, Marina Lotti, Jürgen Pleiss

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  26. eScience Infrastructures in Physical Chemistry

    Annual Review of Physical Chemistry · 2021-12-09

    Samantha Kanza, Cerys Willoughby, Colin Bird, Jeremy Graham Frey

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  27. ROCker Models for Reliable Detection and Typing of Short-Read Sequences Carrying β-Lactamase Genes

    mSystems · 2022-05-31

    Siyu Zhang, Brittany Suttner, Luis M. Rodriguez‐R, Luis H. Orellana, Roth E. Conrad, Fang Cherry Liu, Jessica Lauren Rowell, Hattie E. Webb, Amanda Williams, Andrew D. Huang, Konstantinos T. Konstantinidis

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  28. Machine learning-enabled retrobiosynthesis of molecules

    Nature Catalysis · 2023-02-16

    Tianhao Yu, Aashutosh Girish Boob, Michael Volk, Xuan Liu, Haiyang Cui, Huimin Zhao

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  29. A Novel Pathway for Biosynthesis of the Herbicidal Phosphonate Natural Product Phosphonothrixin Is Widespread in Actinobacteria

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    Luke Bown, Ryuichi Hirota, Michelle N. Goettge, Jerry J. Cui, David T. Krist, Lingyang Zhu, Constantin Giurgiu, Wilfred A. van der Donk, Kou‐San Ju, William W. Metcalf

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  30. Binding Interactions and Inhibition Mechanisms of Gold Complexes in Thiamine Diphosphate-Dependent Enzymes

    Biochemistry · 2023-11-06

    Simon Burgener, Bratislav Dačević, Xiang Zhang, Thomas R. Ward

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  31. Enzyme Databases in the Era of Omics and Artificial Intelligence

    International Journal of Molecular Sciences · 2023-11-29

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  32. Recent trends in biocatalysis and its application in the food industry

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  33. Genome sequencing and molecular networking analysis of the wild fungus Anthostomella pinea reveal its ability to produce a diverse range of secondary metabolites

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  34. FAIR Data and Software: Improving Efficiency and Quality of Biocatalytic Science

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  35. Latest Trends in Lipase-Catalyzed Synthesis of Ester Carbohydrate Surfactants: From Key Parameters to Opportunities and Future Development

    International Journal of Molecular Sciences · 2024-03-27

    Alexis Spalletta, Nicolas Joly, Patrick Martin

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  36. Identification and Characterization of Thiamine Diphosphate‐Dependent Lyases with an Unusual CDG Motif

    Angewandte Chemie International Edition · 2024-06-14

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  37. Identification and Characterization of Thiamine Diphosphate‐Dependent Lyases with an Unusual CDG Motif

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  38. Identification of Kibdelomycin and Related Biosynthetic Gene Clusters and Characterization of the C‐Branching of Amycolose

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  39. Identification of Kibdelomycin and Related Biosynthetic Gene Clusters and Characterization of the C‐Branching of Amycolose

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  40. Digitalization of biocatalysis: Best practices to research data management

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  41. Data-driven revolution of enzyme catalysis from the perspective of reactions, pathways, and enzymes

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  42. Independent evolution of betulin biosynthesis in Inonotus obliquus

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  43. zERExtractor: An Automated Platform for Enzyme-Catalyzed Reaction Data Extraction from Scientific Literature

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  45. Mechanistic insights into activity-enhancing mutations from comparative analysis of two Bacillus subtilis GH11 xylanases

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