The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites
Open accessAbstract
M-CSA (Mechanism and Catalytic Site Atlas) is a database of enzyme active sites and reaction mechanisms that can be accessed at www.ebi.ac.uk/thornton-srv/m-csa. Our objectives with M-CSA are to provide an open data resource for the community to browse known enzyme reaction mechanisms and catalytic sites, and to use the dataset to understand enzyme function and evolution. M-CSA results from the merging of two existing databases, MACiE (Mechanism, Annotation and Classification in Enzymes), a database of enzyme mechanisms, and CSA (Catalytic Site Atlas), a database of catalytic sites of enzymes. We are releasing M-CSA as a new website and underlying database architecture. At the moment, M-CSA contains 961 entries, 423 of these with detailed mechanism information, and 538 with information on the catalytic site residues only. In total, these cover 81% (195/241) of third level EC numbers with a PDB structure, and 30% (840/2793) of fourth level EC numbers with a PDB structure, out of 6028 in total. By searching for close homologues, we are able to extend M-CSA coverage of PDB and UniProtKB to 51 993 structures and to over five million sequences, respectively, of which about 40% and 30% have a conserved active site.
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Caspi, R., Billington, R., Ferrer, L., Foerster, H., Fulcher, C. A., Keseler, I. M., Kothari, A., Krummenacker, M., Latendresse, M., Mueller, L. A., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1164 · Cited by 3,395
The relation between the divergence of sequence and structure in proteins.
Chothia, C., & Lesk, A. M. (1986) · The EMBO Journal · doi:10.1002/j.1460-2075.1986.tb04288.x · Cited by 2,458
Updates in Rhea—An expert curated resource of biochemical reactions
Morgat, A., Lombardot, T., Axelsen, K. B., Aimo, L., Niknejad, A., Hyka-Nouspikel, N., Coudert, E., Pozzato, M., Pagni, M., Moretti, S., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw990 · Cited by 65
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Watson, J. L., Juergens, D., Bennett, N. R., Trippe, B. L., Yim, J., Eisenach, H. E., Ahern, W., Borst, A. J., Ragotte, R. J., Milles, L. F., et al. (2022) · doi:10.1101/2022.12.09.519842 · Cited by 2,369
De novo design of protein structure and function with RFdiffusion
Watson, J. L., Juergens, D., Bennett, N. R., Trippe, B. L., Yim, J., Eisenach, H. E., Ahern, W., Borst, A. J., Ragotte, R. J., Milles, L. F., et al. (2023) · Nature · doi:10.1038/s41586-023-06415-8 · Cited by 2,325
The Hitchhiker's guide to biocatalysis: recent advances in the use of enzymes in organic synthesis
Sheldon, R. A., Brady, D., & Bode, M. L. (2020) · Chemical Science · doi:10.1039/c9sc05746c · Cited by 299
Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport
Stourac, J., Vavra, O., Kokkonen, P., Filipovic, J., Pinto, G., Brezovsky, J., Damborsky, J., & Bednar, D. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz378 · Cited by 267
Rhea, the reaction knowledgebase in 2022
Bansal, P., Morgat, A., Axelsen, K. B., Muthukrishnan, V., Coudert, E., Aimo, L., Hyka-Nouspikel, N., Gasteiger, E., Kerhornou, A., Neto, T. B., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab1016 · Cited by 253
Metadata
- Authors
- Ribeiro, A. J. M., Holliday, G. L., Furnham, N., Tyzack, J. D., Ferris, K., & Thornton, J. M.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2017-11-02
- Volume
- 46
- Issue
- D1
- Pages
- D618-D623
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2765284721
- Cited by
- 235
- References
- 3
- FWCI
- 4.74
- Type
- journal article
- Language
- en
- Open access
- gold
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- Ribeiro, A. J. M., Holliday, G. L., Furnham, N., Tyzack, J. D., Ferris, K., & Thornton, J. M. (2018). Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites. Nucleic Acids Research. https://doi.org/10.1093/nar/gkx1012
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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