PathPred: an enzyme-catalyzed metabolic pathway prediction server
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Summary
This server presents PathPred, a web-based server to predict plausible pathways of muti-step reactions starting from a query compound, based on the local RDM pattern match and the global chemical structure alignment against the reactant pair library.
- Type
- article
- Published
- 2010-04-30
- Cited by
- 240
- References
- 12
- Access
- Open access
- OpenAlex
- https://openalex.org/W1997996256
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:13070150
Keywords
KEGG, RDM, Biology, Metabolic pathway, Computational biology
References
- Organizing and computing metabolic pathway data in terms of binary relations.
- Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways.
- Computational assignment of the EC numbers for genomic-scale analysis of enzymatic reactions.
- SIMCOMP/SUBCOMP: chemical structure search servers for network analyses
- ExplorEnz: the primary source of the IUBMB enzyme list
- The University of Minnesota Biocatalysis/Biodegradation Database: improving public access
- KAAS: an automatic genome annotation and pathway reconstruction server
- Data-driven extraction of relative reasoning rules to limit combinatorial explosion in biodegradation pathway prediction
- E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs
- KEGG for representation and analysis of molecular networks involving diseases and drugs
- Systematic Analysis of Enzyme-Catalyzed Reaction Patterns and Prediction of Microbial Biodegradation Pathways
- Nucleic Acids Research
Cited by
- The KEGG databases and tools facilitating omics analysis: latest developments involving human diseases and pharmaceuticals.
- Computational Methods in Metabolomics
- Systems Metabolic Engineering of Escherichia coli
- Cheminformatics for genome-scale metabolic reconstructions
- The chemistry and evolution of enzyme function: isomerases as a case study
- An efficient algorithm for de novo predictions of biochemical pathways between chemical compounds
- CMPF: Class-switching minimized pathfinding in metabolic networks
- Phenomic and genomic diversity of a bacterial species in a local population
- Genome Sequence Analysis of the Naphthenic Acid Degrading and Metal Resistant Bacterium Cupriavidus gilardii CR3
- MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics
- Metabolic Pathway Predictions for Metabolomics: A Molecular Structure Matching Approach
- Predictive genomic and metabolomic analysis for the standardization of enzyme data
- Systems metabolic engineering of microorganisms for natural and non-natural chemicals.
- Aerobic degradation of aromatic compounds.
- Rational identification of diet-derived postbiotics for improving intestinal microbiota function.
- MUCHA: multiple chemical alignment algorithm to identify building block substructures of orphan secondary metabolites
- Computational methods in metabolic engineering for strain design.
- Probabilistic pathway construction.
- A tiered procedure for assessing the formation of biotransformation products of pharmaceuticals and biocides during activated sludge treatment.
- Design Automation for Synthetic Biological Systems
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