Mechanism and Catalytic Site Atlas
Names
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Mechanism and Catalytic Site Atlas
metasource: Fairsharing.org
version: FAIRsharing.org: M-CSA; Mechanism and Catalytic Site Atlas; DOI: https://doi.org/10.25504/FAIRsharing.BrubDI; Last edited: May 4, 2020, 11:08 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: re3data.org
version: re3data.org: Mechanism and Catalytic Site Atlas; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CW39 last accessed: 2022-11-04
M-CSA
metasource: Fairsharing.org
version: FAIRsharing.org: M-CSA; Mechanism and Catalytic Site Atlas; DOI: https://doi.org/10.25504/FAIRsharing.BrubDI; Last edited: May 4, 2020, 11:08 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: Mechanism and Catalytic Site Atlas; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CW39 last accessed: 2022-11-04
CSA (formerly)
metasource: re3data.org
version: re3data.org: Mechanism and Catalytic Site Atlas; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CW39 last accessed: 2022-11-04
Catalytic Site Atlas (formerly)
metasource: re3data.org
version: re3data.org: Mechanism and Catalytic Site Atlas; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CW39 last accessed: 2022-11-04
Names
More detailed information about this field from each metasource.
Mechanism and Catalytic Site Atlas
metasource: Fairsharing.orgversion: FAIRsharing.org: M-CSA; Mechanism and Catalytic Site Atlas; DOI: https://doi.org/10.25504/FAIRsharing.BrubDI; Last edited: May 4, 2020, 11:08 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: re3data.org
version: re3data.org: Mechanism and Catalytic Site Atlas; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CW39 last accessed: 2022-11-04
M-CSA
metasource: Fairsharing.orgversion: FAIRsharing.org: M-CSA; Mechanism and Catalytic Site Atlas; DOI: https://doi.org/10.25504/FAIRsharing.BrubDI; Last edited: May 4, 2020, 11:08 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: Mechanism and Catalytic Site Atlas; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CW39 last accessed: 2022-11-04
CSA (formerly)
metasource: re3data.orgversion: re3data.org: Mechanism and Catalytic Site Atlas; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CW39 last accessed: 2022-11-04
Catalytic Site Atlas (formerly)
metasource: re3data.orgversion: re3data.org: Mechanism and Catalytic Site Atlas; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CW39 last accessed: 2022-11-04
Other names: M-CSA, CSA (formerly), Catalytic Site Atlas (formerly)
Names
More detailed information about this field from each metasource.
Mechanism and Catalytic Site Atlas
metasource: Fairsharing.orgversion: FAIRsharing.org: M-CSA; Mechanism and Catalytic Site Atlas; DOI: https://doi.org/10.25504/FAIRsharing.BrubDI; Last edited: May 4, 2020, 11:08 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: re3data.org
version: re3data.org: Mechanism and Catalytic Site Atlas; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CW39 last accessed: 2022-11-04
M-CSA
metasource: Fairsharing.orgversion: FAIRsharing.org: M-CSA; Mechanism and Catalytic Site Atlas; DOI: https://doi.org/10.25504/FAIRsharing.BrubDI; Last edited: May 4, 2020, 11:08 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: Mechanism and Catalytic Site Atlas; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CW39 last accessed: 2022-11-04
CSA (formerly)
metasource: re3data.orgversion: re3data.org: Mechanism and Catalytic Site Atlas; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CW39 last accessed: 2022-11-04
Catalytic Site Atlas (formerly)
metasource: re3data.orgversion: re3data.org: Mechanism and Catalytic Site Atlas; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CW39 last accessed: 2022-11-04
M-CSA is a database of enzyme reaction mechanisms. It provides annotation on the protein, catalytic residues, cofactors, and the reaction mechanisms of hundreds of enzymes. There are two kinds of entries in M-CSA: 'Detailed mechanism' entries are more complete and show the individual chemical steps of the mechanism as schemes with electron flow arrows; and 'Catalytic Site' entries annotate the catalytic residues necessary for the reaction, but do not show the mechanism.
Description
More detailed information about this field from each metasource.
M-CSA is a database of enzyme reaction mechanisms. It provides annotation on the protein, catalytic residues, cofactors, and the reaction mechanisms of hundreds of enzymes. There are two kinds of entries in M-CSA: 'Detailed mechanism' entries are more complete and show the individual chemical steps of the mechanism as schemes with electron flow arrows; and 'Catalytic Site' entries annotate the catalytic residues necessary for the reaction, but do not show the mechanism.
metasource: Fairsharing.orgversion: FAIRsharing.org: M-CSA; Mechanism and Catalytic Site Atlas; DOI: https://doi.org/10.25504/FAIRsharing.BrubDI; Last edited: May 4, 2020, 11:08 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
M-CSA is a database of enzyme reaction mechanisms. It provides annotation on the protein, catalytic residues, cofactors, and the reaction mechanisms of hundreds of enzymes. There are two kinds of entries in M-CSA. 'Detailed mechanism' entries are more complete and show the individual chemical steps of the mechanism as schemes with electron flow arrows. 'Catalytic Site' entries annotate the catalytic residues necessary for the reaction, but do not show the mechanism. The M-CSA (Mechanism and Catalytic Site Atlas) represents a unified resource that combines the data in both MACiE and the CSA
metasource: re3data.orgversion: re3data.org: Mechanism and Catalytic Site Atlas; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CW39 last accessed: 2022-11-04
Webpage:
https://www.ebi.ac.uk/thornton-srv/m-csa/Webpage
More detailed information about this field from each metasource.
https://www.ebi.ac.uk/thornton-srv/m-csa/
metasource: Fairsharing.orgversion: FAIRsharing.org: M-CSA; Mechanism and Catalytic Site Atlas; DOI: https://doi.org/10.25504/FAIRsharing.BrubDI; Last edited: May 4, 2020, 11:08 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://www.ebi.ac.uk/thornton-srv/m-csa
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
https://www.ebi.ac.uk/thornton-srv/m-csa/Dine26!2
metasource: re3data.orgversion: re3data.org: Mechanism and Catalytic Site Atlas; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CW39 last accessed: 2022-11-04
Licence:
Name: Creative Commons Attribution-NoDerivs 3.0 Unported (CC BY-ND 3.0)Licence name
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Creative Commons Attribution-NoDerivs 3.0 Unported (CC BY-ND 3.0)
metasource: Fairsharing.orgversion: FAIRsharing.org: M-CSA; Mechanism and Catalytic Site Atlas; DOI: https://doi.org/10.25504/FAIRsharing.BrubDI; Last edited: May 4, 2020, 11:08 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
CC
metasource: re3data.orgversion: re3data.org: Mechanism and Catalytic Site Atlas; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CW39 last accessed: 2022-11-04
Licence URL
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https://creativecommons.org/licenses/by-nd/3.0/
metasource: Fairsharing.orgversion: FAIRsharing.org: M-CSA; Mechanism and Catalytic Site Atlas; DOI: https://doi.org/10.25504/FAIRsharing.BrubDI; Last edited: May 4, 2020, 11:08 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://creativecommons.org/licenses/by-nd/3.0/
metasource: re3data.orgversion: re3data.org: Mechanism and Catalytic Site Atlas; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CW39 last accessed: 2022-11-04
Publications:
Publications
More detailed information about this field from each metasource.
Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites
PMID: 29106569
metasource: Fairsharing.org
version: FAIRsharing.org: M-CSA; Mechanism and Catalytic Site Atlas; DOI: https://doi.org/10.25504/FAIRsharing.BrubDI; Last edited: May 4, 2020, 11:08 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://dx.doi.org/10.1093/nar/gkx1012
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites
PMID: 29106569
metasource: Fairsharing.org
version: FAIRsharing.org: M-CSA; Mechanism and Catalytic Site Atlas; DOI: https://doi.org/10.25504/FAIRsharing.BrubDI; Last edited: May 4, 2020, 11:08 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://dx.doi.org/10.1093/nar/gkx1012
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites
PubMed citations: 42.
42 articles citing: Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites
Menthol carbonates as potent antiparasitic agents: synthesis and in vitro studies along with computer-aided approaches. PMID:35698116
Electrostatic fingerprints of catalytically active amino acids in enzymes. PMID:35481659
3DLigandSite: structure-based prediction of protein-ligand binding sites. PMID:35412635
Protein cost minimization promotes the emergence of coenzyme redundancy. PMID:35344442
Conformational Variation in Enzyme Catalysis: A Structural Study on Catalytic Residues. PMID:35240125
Florigen and its homologs of FT/CETS/PEBP/RKIP/YbhB family may be the enzymes of small molecule metabolism: review of the evidence. PMID:35086479
Worldwide Protein Data Bank (wwPDB): A virtual treasure for research in biotechnology. PMID:34908533
A roadmap for metagenomic enzyme discovery. PMID:34821235
Rhea, the reaction knowledgebase in 2022. PMID:34755880
PDBe-KB: collaboratively defining the biological context of structural data. PMID:34755867
Machine learning for enzyme engineering, selection and design. PMID:34296736
Graph transformation for enzymatic mechanisms. PMID:34252947
Machine learning differentiates enzymatic and non-enzymatic metals in proteins. PMID:34140507
BENZ WS: the Bologna ENZyme Web Server for four-level EC number annotation. PMID:33963861
Quantifying evolutionary importance of protein sites: A Tale of two measures. PMID:33826605
Addressing uncertainty in genome-scale metabolic model reconstruction and analysis. PMID:33602294
Water and Life: The Medium is the Message. PMID:33427903
An automated protocol for modelling peptide substrates to proteases. PMID:33375946
The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies. PMID:33348379
FireProtASR: A Web Server for Fully Automated Ancestral Sequence Reconstruction. PMID:33346815
Real-time structural motif searching in proteins using an inverted index strategy. PMID:33284792
CATH functional families predict functional sites in proteins. PMID:33135053
A strategy for large-scale comparison of evolutionary- and reaction-based classifications of enzyme function. PMID:32449511
The Hitchhiker's guide to biocatalysis: recent advances in the use of enzymes in organic synthesis. PMID:32206264
Developing and applying computational resources for biochemistry education. PMID:32203640
Autocatalytic chemical networks at the origin of metabolism. PMID:32156207
A Benchmark for Homomeric Enzyme Active Site Structure Prediction Highlights the Importance of Accurate Modeling of Protein Symmetry. PMID:31909318
A global analysis of function and conservation of catalytic residues in enzymes. PMID:31796628
Environmental boundary conditions for the origin of life converge to an organo-sulfur metabolism. PMID:31712697
MANET 3.0: Hierarchy and modularity in evolving metabolic networks. PMID:31648227
Challenges in the annotation of pseudoenzymes in databases: the UniProtKB approach. PMID:31618524
PDBe-KB: a community-driven resource for structural and functional annotations. PMID:31584092
funtrp: identifying protein positions for variation driven functional tuning. PMID:31584091
VarMap: a web tool for mapping genomic coordinates to protein sequence and structure and retrieving protein structural annotations. PMID:31192369
Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport. PMID:31114897
Characterization of recombinant endo-1,4-β-xylanase of Bacillus halodurans C-125 and rational identification of hot spot amino acid residues responsible for enhancing thermostability by an in-silico approach. PMID:31079316
PIRSitePredict for protein functional site prediction using position-specific rules. PMID:30805646
CATH: expanding the horizons of structure-based functional annotations for genome sequences. PMID:30398663
Updates in Rhea: SPARQLing biochemical reaction data. PMID:30272209
Ranking Enzyme Structures in the PDB by Bound Ligand Similarity to Biological Substrates. PMID:29551288
The 2018 Nucleic Acids Research database issue and the online molecular biology database collection. PMID:29316735
The European Bioinformatics Institute in 2017: data coordination and integration. PMID:29186510 - http://dx.doi.org/10.1093/nar/gkx1012
Tags:
Tags
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annotation
metasource: Fairsharing.org
version: FAIRsharing.org: M-CSA; Mechanism and Catalytic Site Atlas; DOI: https://doi.org/10.25504/FAIRsharing.BrubDI; Last edited: May 4, 2020, 11:08 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
catalytic activity
metasource: Fairsharing.org
version: FAIRsharing.org: M-CSA; Mechanism and Catalytic Site Atlas; DOI: https://doi.org/10.25504/FAIRsharing.BrubDI; Last edited: May 4, 2020, 11:08 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
enzymatic reaction
metasource: Fairsharing.org
version: FAIRsharing.org: M-CSA; Mechanism and Catalytic Site Atlas; DOI: https://doi.org/10.25504/FAIRsharing.BrubDI; Last edited: May 4, 2020, 11:08 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
enzyme
metasource: Fairsharing.org
version: FAIRsharing.org: M-CSA; Mechanism and Catalytic Site Atlas; DOI: https://doi.org/10.25504/FAIRsharing.BrubDI; Last edited: May 4, 2020, 11:08 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metabolic and signaling pathways
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
enzymes and enzyme nomenclature
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
3d structure
metasource: re3data.org
version: re3data.org: Mechanism and Catalytic Site Atlas; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CW39 last accessed: 2022-11-04
activation (chemistry)
metasource: re3data.org
version: re3data.org: Mechanism and Catalytic Site Atlas; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CW39 last accessed: 2022-11-04
amino acids
metasource: re3data.org
version: re3data.org: Mechanism and Catalytic Site Atlas; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CW39 last accessed: 2022-11-04
catalysis
metasource: re3data.org
version: re3data.org: Mechanism and Catalytic Site Atlas; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CW39 last accessed: 2022-11-04
enzymes
metasource: re3data.org
version: re3data.org: Mechanism and Catalytic Site Atlas; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CW39 last accessed: 2022-11-04
proteins
metasource: re3data.org
version: re3data.org: Mechanism and Catalytic Site Atlas; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CW39 last accessed: 2022-11-04
Tags
More detailed information about this field from each metasource.
annotation
metasource: Fairsharing.orgversion: FAIRsharing.org: M-CSA; Mechanism and Catalytic Site Atlas; DOI: https://doi.org/10.25504/FAIRsharing.BrubDI; Last edited: May 4, 2020, 11:08 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
catalytic activity
metasource: Fairsharing.orgversion: FAIRsharing.org: M-CSA; Mechanism and Catalytic Site Atlas; DOI: https://doi.org/10.25504/FAIRsharing.BrubDI; Last edited: May 4, 2020, 11:08 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
enzymatic reaction
metasource: Fairsharing.orgversion: FAIRsharing.org: M-CSA; Mechanism and Catalytic Site Atlas; DOI: https://doi.org/10.25504/FAIRsharing.BrubDI; Last edited: May 4, 2020, 11:08 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
enzyme
metasource: Fairsharing.orgversion: FAIRsharing.org: M-CSA; Mechanism and Catalytic Site Atlas; DOI: https://doi.org/10.25504/FAIRsharing.BrubDI; Last edited: May 4, 2020, 11:08 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metabolic and signaling pathways
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
enzymes and enzyme nomenclature
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
3d structure
metasource: re3data.orgversion: re3data.org: Mechanism and Catalytic Site Atlas; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CW39 last accessed: 2022-11-04
activation (chemistry)
metasource: re3data.orgversion: re3data.org: Mechanism and Catalytic Site Atlas; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CW39 last accessed: 2022-11-04
amino acids
metasource: re3data.orgversion: re3data.org: Mechanism and Catalytic Site Atlas; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CW39 last accessed: 2022-11-04
catalysis
metasource: re3data.orgversion: re3data.org: Mechanism and Catalytic Site Atlas; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CW39 last accessed: 2022-11-04
enzymes
metasource: re3data.orgversion: re3data.org: Mechanism and Catalytic Site Atlas; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CW39 last accessed: 2022-11-04
proteins
metasource: re3data.orgversion: re3data.org: Mechanism and Catalytic Site Atlas; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CW39 last accessed: 2022-11-04
catalytic activity enzymatic reaction enzyme metabolic and signaling pathways enzymes and enzyme nomenclature 3d structure activation (chemistry) amino acids catalysis enzyme proteins
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