Masters Thesis Data

This is all the data required for reproducing the results of my Masters Thesis.

Data collected from the following sources:

Datasets 1-3 were extracted from uniprot:

Dataset 1: All experimentally derived Catalytic Residue annotations in UniProt or SwissProt databases.

Dataset 2: Experimentally validated and reviewed SwissProt sequences that have known experimentally derived  structures.

Dataset 3: All reviewed and experimental annotations from the SwissProt database.

T. U. Consortium, “UniProt: the Universal Protein Knowledgebase in2023,” Nucleic Acids Research, vol. 51, no. D1, pp. D523–D531, Nov. 2022,ISSN: 0305-1048. DOI: 10.1093/nar/gkac1052. eprint: https://academic.oup.com/nar/article- pdf/51/D1/D523/48441158/gkac1052.pdf. [Online]. Available: https://doi.org/10.1093/nar/gkac1052

Case study 1 metagenomic files:

D. Dai, C. Brown, H. Bürgmann, et al., “Long-read metagenomic se-quencing reveals shifts in associations of antibiotic resistance geneswith mobile genetic elements from sewage to activated sludge,” Mi-crobiome, vol. 10, no. 1, p. 20, Jan. 2022, ISSN: 2049-2618. DOI: 10.1186/s40168-021-01216-5. [Online]. Available: https://doi.org/10.1186/s40168-021-01216-5

MDH, CuSOD, CM fast files:

S. R. Johnson, X. Fu, S. Viknander, et al., “Computational scoring and experimental evaluation of enzymes generated by neural networks,” Nature Biotechnology, Apr. 2024, ISSN: 1546-1696. DOI: 10.1038/s41587-024-02214-2. [Online]. Available: https://doi.org/10.1038/s41587-024-02214-2

Literature sequences for case study 1:

Xu, Y.; Liu, X.; Zhao, J.; Huang, H.; Wu, M.; Li, X.; Li, W.; Sun, X.; Sun, B. An Efficient Phthalate Ester-Degrading Bacillus Subtilis: Degradation Kinetics, Metabolic Pathway, and Catalytic Mechanism of the Key Enzyme. Environmental Pollution 2021, 273, 116461. https://doi.org/10.1016/j.envpol.2021.116461.

Cheng, J.; Du, H.; Zhou, M.-S.; Ji, Y.; Xie, Y.-Q.; Huang, H.-B.; Zhang, S.-H.; Li, F.; Xiang, L.; Cai, Q.-Y.; Li, Y.-W.; Li, H.; Li, M.; Zhao, H.-M.; Mo, C.-H. Substrate‐enzyme Interactions and Catalytic Mechanism in a Novel Family VI Esterase with Dibutyl Phthalate-Hydrolyzing Activity. Environment International 2023, 178, 108054. https://doi.org/10.1016/j.envint.2023.108054.

Qiu, J.; Zhang, Y.; Shi, Y.; Jiang, J.; Wu, S.; Li, L.; Shao, Y.; Xin, Z. Identification and Characterization of a Novel Phthalate-Degrading Hydrolase from a Soil Metagenomic Library. Ecotoxicology and Environmental Safety 2020, 190, 110148.