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UM-BBD specifications


Unique identifier OMICS_21394
Alternative name University of Minnesota Biocatalysis/Biodegradation Database
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 1.0
Maintained No


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Publication for University of Minnesota Biocatalysis/Biodegradation Database

UM-BBD citations


Production of C2–C4 diols from renewable bioresources: new metabolic pathways and metabolic engineering strategies

Biotechnol Biofuels
PMCID: 5727944
PMID: 29255482
DOI: 10.1186/s13068-017-0992-9

[…] ioresources. There are no known natural pathways to directly synthesize EG from sugars. Based on partially known d-xylonate catabolism and in silico analysis using the metabolite prediction system of UM-BBD (University of Minnesota Biocatalysis and Biodegradation Database), Liu et al. have proposed a d-xylonate-dependent pathway (modified Dahms pathway) and demonstrated the first example of EG bio […]


A review of computational tools for design and reconstruction of metabolic pathways

PMCID: 5851934
PMID: 29552648
DOI: 10.1016/j.synbio.2017.11.002

[…] titute the pathway of interest. Currently, a number of databases have been constructed for known biochemical reactions and pathways (i.e., BIGG , KEGG , MetaCyc , BRENDA , ModelSEED , MetRxn , Rhea , UM-BBD , MOS , and Beilste Crossfile ), as well as hypothetical metabolites and reactions (such as ATLAS of Biochemistry , and MINE ) (see A). The current version of BIGG database consists of 80 manua […]


Searching for “Environmentally Benign” Antifouling Biocides

Int J Mol Sci
PMCID: 4100093
PMID: 24865489
DOI: 10.3390/ijms15069255

[…] nds was compared against the literature or MSDS toxicity data whenever available.Biodegradation pathway of diuron was predicted using the University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD, list of pharmaceuticals medicines and its biological data in was obtained from a study published by Rittschof et. al. [] and Dahlström et al. []. The […]


Integer Programming Based Method for Designing Synthetic Metabolic Networks by Minimum Reaction Insertion in a Boolean Model

PLoS One
PMCID: 3961429
PMID: 24651476
DOI: 10.1371/journal.pone.0092637

[…] tworks, while (b) and (c) utilize the information of the structures of chemicals as well.The “pathway prediction system” (PPS) of the University of Minnesota Biocatalysis and Biodegradation Database (UM-BBD) is designed to predict routes for the biodegradation of xenobiotic compounds –. From a set of previously defined biotransformation rules, the PPS guides the user through potential pathways one […]


Applications of Natural Language Processing in Biodiversity Science

Adv Bioinformatics
PMCID: 3364545
PMID: 22685456
DOI: 10.1155/2012/391574

[…] attern matching that focuses on finding words in text that are contained in a dictionary previously given to the computer. For example, the computer might be given a list of enzyme names (such as the UM-BBD list of enzyme names,; X in previous example). Once the enzyme name is located, the computer can infer the pattern that it “activa […]


In silico feasibility of novel biodegradation pathways for 1,2,4 trichlorobenzene

BMC Syst Biol
PMCID: 2830930
PMID: 20122273
DOI: 10.1186/1752-0509-4-7
call_split See protocol

[…] el reactions.We employed BNICE to generate novel biodegradation pathways for 1,2,4-trichlorobenzene. We determined the enzyme reaction rules necessary to reproduce the known pathway catalogued in the UM-BBD and implemented those rules into the BNICE framework in order to generate novel routes to compounds with known intermediary metabolism. Ten reaction rules were required to reproduce the known p […]


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UM-BBD institution(s)
Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA; Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St Paul, MN, USA
UM-BBD funding source(s)
Supported by US National Science Foundation (NSF0543416) and the Minnesota Supercomputing Institute.

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