R33C9X last accessed: 2022-11-04

SABIO-RK: biochemical reactions and their kinetics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:23.842818

sabio-rk
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:23.842818

Other names: SABIO-RK, Biochemical reation kinetics database, System for the Analysis of Biochemical Pathways - Reaction Kinetics, SABIO-RK: biochemical reactions and their kinetics, sabio-rk

SABIO-RK is a database for biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured.

Webpage:

http://sabiork.h-its.org/

Licence:

Name: Open Data Commons (ODC) Public Domain Dedication and Licence (PDDL) 1.0
URL: http://opendatacommons.org/licenses/pddl/1.0/

Publications:

Publications
More detailed information about this field from each metasource.

SABIO-RK--database for biochemical reaction kinetics
PMID: 22102587
metasource: Fairsharing.org
version: FAIRsharing.org: SABIO-RK; SABIO-RK Biochemical Reaction Kinetics Database; DOI: https://doi.org/10.25504/FAIRsharing.cwx04e; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

http://dx.doi.org/10.1093/nar/GKR1046
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

http://dx.doi.org/10.1093/nar/gkr1046
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:23.842818

http://dx.doi.org/10.1093/nar/gkx1065
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:23.842818

SABIO-RK--database for biochemical reaction kinetics PubMed citations: 85.

85 articles citing: SABIO-RK--database for biochemical reaction kinetics

Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows. PMID:35792600
Boolean modelling as a logic-based dynamic approach in systems medicine. PMID:35782730
Fluxomics - New Metabolomics Approaches to Monitor Metabolic Pathways. PMID:35387341
Kinetic and Stoichiometric Modeling-Based Analysis of Docosahexaenoic Acid (DHA) Production Potential by Crypthecodinium cohnii from Glycerol, Glucose and Ethanol. PMID:35200644
Deep learning allows genome-scale prediction of Michaelis constants from structural features. PMID:34665809
Music of metagenomics-a review of its applications, analysis pipeline, and associated tools. PMID:34657989
A protocol for dynamic model calibration. PMID:34619769
PncsHub: a platform for annotating and analyzing non-classically secreted proteins in Gram-positive bacteria. PMID:34551435
The effects of model complexity and size on metabolic flux distribution and control: case study in Escherichia coli. PMID:33743594
Proteome Regulation Patterns Determine Escherichia coli Wild-Type and Mutant Phenotypes. PMID:33688016
The Metano Modeling Toolbox MMTB: An Intuitive, Web-Based Toolbox Introduced by Two Use Cases. PMID:33671140
KiMoSys 2.0: an upgraded database for submitting, storing and accessing experimental data for kinetic modeling. PMID:33247931
BRENDA, the ELIXIR core data resource in 2021: new developments and updates. PMID:33211880
Bioengineering studies and pathway modeling of the heterologous biosynthesis of tetrahydrocannabinolic acid in yeast. PMID:33043390
Computer-Aided Whole-Cell Design: Taking a Holistic Approach by Integrating Synthetic With Systems Biology. PMID:32850764
Common biochemical properties of metabolic genes recurrently dysregulated in tumors. PMID:32411371
Gene-Wise Burden of Coding Variants Correlates to Noncoding Pharmacogenetic Risk Variants. PMID:32349395
The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models. PMID:31937763
Automatic construction of metabolic models with enzyme constraints. PMID:31937255
Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices. PMID:31602618
ModelBricks-modules for reproducible modeling improving model annotation and provenance. PMID:31602314
Uncertainty reduction in biochemical kinetic models: Enforcing desired model properties. PMID:31430276
Kinetic modeling of Stickland reactions-coupled methanogenesis for a methanogenic culture. PMID:31183623
Reproducible pharmacokinetics. PMID:31004315
Consistency, Inconsistency, and Ambiguity of Metabolite Names in Biochemical Databases Used for Genome-Scale Metabolic Modelling. PMID:30736318
Integration of enzymatic data in Bacillus subtilis genome-scale metabolic model improves phenotype predictions and enables in silico design of poly-γ-glutamic acid production strains. PMID:30626384
Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models. PMID:30531987
Harmonizing semantic annotations for computational models in biology. PMID:30462164
BRENDA in 2019: a European ELIXIR core data resource. PMID:30395242
A Review of Dynamic Modeling Approaches and Their Application in Computational Strain Optimization for Metabolic Engineering. PMID:30108559
In Silico Prediction of Large-Scale Microbial Production Performance: Constraints for Getting Proper Data-Driven Models. PMID:30105090
DMPy: a Python package for automated mathematical model construction of large-scale metabolic systems. PMID:29914475
A review of computational tools for design and reconstruction of metabolic pathways. PMID:29552648
From correlation to causation: analysis of metabolomics data using systems biology approaches. PMID:29503602
STRENDA DB: enabling the validation and sharing of enzyme kinetics data. PMID:29498804
Emerging whole-cell modeling principles and methods. PMID:29275251
Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites. PMID:29106569
SABIO-RK: an updated resource for manually curated biochemical reaction kinetics. PMID:29092055
A Protocol for Generating and Exchanging (Genome-Scale) Metabolic Resource Allocation Models. PMID:28878200
Elucidation of the molecular mechanisms underlying adverse reactions associated with a kinase inhibitor using systems toxicology. PMID:28725458
Cellular trade-offs and optimal resource allocation during cyanobacterial diurnal growth. PMID:28720699
biochem4j: Integrated and extensible biochemical knowledge through graph databases. PMID:28708831
SBMLmod: a Python-based web application and web service for efficient data integration and model simulation. PMID:28646877
ChloroKB: A Web Application for the Integration of Knowledge Related to Chloroplast Metabolic Network. PMID:28442501
Mathematical analysis of the influence of brain metabolism on the BOLD signal in Alzheimer's disease. PMID:28271954
Protein Bioinformatics Databases and Resources. PMID:28150231
Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks. PMID:28114351
A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains. PMID:27996047
FAIRDOMHub: a repository and collaboration environment for sharing systems biology research. PMID:27899646
Genome Sequence Variability Predicts Drug Precautions and Withdrawals from the Market. PMID:27690231
The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable. PMID:27051515
A physiome interoperability roadmap for personalized drug development. PMID:27051513
ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis. PMID:26882475
Predictive Modeling of Drug Treatment in the Area of Personalized Medicine. PMID:26692759
SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks. PMID:26452770
Diversity in protein domain superfamilies. PMID:26451979
BioModels: Content, Features, Functionality, and Use. PMID:26225232
SEEK: a systems biology data and model management platform. PMID:26160520
kpath: integration of metabolic pathway linked data. PMID:26055101
Mathematical modelling of metabolic regulation in aging. PMID:25923415
Computationally Modeling Lipid Metabolism and Aging: A Mini-review. PMID:25750699
Computational modeling of drug response with applications to neuroscience. PMID:25733952
Quantitative and logic modelling of molecular and gene networks. PMID:25645874
Synthetic biology outside the cell: linking computational tools to cell-free systems. PMID:25538941
Self-organization of signal transduction. PMID:25506419
Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. PMID:25503938
Predictive sulfur metabolism - a field in flux. PMID:25477892
LigDig: a web server for querying ligand-protein interactions. PMID:25433696
BioModels: ten-year anniversary. PMID:25414348
BioModels linked dataset. PMID:25182954
KiMoSys: a web-based repository of experimental data for KInetic MOdels of biological SYStems. PMID:25115331
Text-mining-assisted biocuration workflows in Argo. PMID:25037308
What mRNA Abundances Can Tell us about Metabolism. PMID:24957650
Large-scale determination of sequence, structure, and function relationships in cytosolic glutathione transferases across the biosphere. PMID:24756107
Identification of key regulators in glycogen utilization in E. coli based on the simulations from a hybrid functional Petri net model. PMID:24565082
The future of whole-cell modeling. PMID:24556244
A systems' biology approach to study microRNA-mediated gene regulatory networks. PMID:24350286
Path2Models: large-scale generation of computational models from biochemical pathway maps. PMID:24180668
Function of dynamic models in systems biology: linking structure to behaviour. PMID:24103739
Structure, function, and behaviour of computational models in systems biology. PMID:23721297
Towards the collaborative curation of the registry underlying Identifiers.org. PMID:23584831
Precise generation of systems biology models from KEGG pathways. PMID:23433509
WholeCellKB: model organism databases for comprehensive whole-cell models. PMID:23175606
Shrinking the metabolic solution space using experimental datasets. PMID:22956899
Multiscale modeling and data integration in the virtual physiological rat project. PMID:22805979
http://dx.doi.org/10.1093/nar/GKR1046
http://dx.doi.org/10.1093/nar/gkr1046
http://dx.doi.org/10.1093/nar/gkx1065

Tags:

Tags
More detailed information about this field from each metasource.

enzyme
metasource: Fairsharing.org
version: FAIRsharing.org: SABIO-RK; SABIO-RK Biochemical Reaction Kinetics Database; DOI: https://doi.org/10.25504/FAIRsharing.cwx04e; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

reaction data
metasource: Fairsharing.org
version: FAIRsharing.org: SABIO-RK; SABIO-RK Biochemical Reaction Kinetics Database; DOI: https://doi.org/10.25504/FAIRsharing.cwx04e; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:07 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

biochemical reactions
metasource: re3data.org
version: re3data.org: SABIO-RK; editing status 2021-11-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R33C9X last accessed: 2022-11-04

biology
metasource: re3data.org
version: re3data.org: SABIO-RK; editing status 2021-11-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R33C9X last accessed: 2022-11-04

metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:23.842818

enzyme kinetics
metasource: re3data.org
version: re3data.org: SABIO-RK; editing status 2021-11-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R33C9X last accessed: 2022-11-04

kinetic equations
metasource: re3data.org
version: re3data.org: SABIO-RK; editing status 2021-11-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R33C9X last accessed: 2022-11-04

kinetic properties
metasource: re3data.org
version: re3data.org: SABIO-RK; editing status 2021-11-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R33C9X last accessed: 2022-11-04

medicine
metasource: re3data.org
version: re3data.org: SABIO-RK; editing status 2021-11-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R33C9X last accessed: 2022-11-04

molecular biology
metasource: re3data.org
version: re3data.org: SABIO-RK; editing status 2021-11-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R33C9X last accessed: 2022-11-04

proteins
metasource: re3data.org
version: re3data.org: SABIO-RK; editing status 2021-11-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R33C9X last accessed: 2022-11-04

systems biology
metasource: re3data.org
version: re3data.org: SABIO-RK; editing status 2021-11-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R33C9X last accessed: 2022-11-04

metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:23.842818

biochemistry
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:23.842818

data mining
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:23.842818

biomedical science
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:23.842818

enzymes
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:23.842818

data submission, annotation and curation
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:23.842818

molecular interactions, pathways and networks
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:23.842818

enzyme reaction data metabolic and signaling pathways enzymes and enzyme nomenclature biochemical reactions enzyme kinetics kinetic equations kinetic properties medicine molecular biology proteins systems biology biochemistry data mining biomedical science enzyme data submission, annotation and curation molecular interactions, pathways and networks

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