Biocatalysis/Biodegradation database
The Biocatalysis/Biodegradation database (BBD) has compiled information on microbial enzyme‐catalyzed reactions that are useful for synthetic purposes or function in biodegradation pathways to remove chemicals from environmental compartments.
Pathway Prediction System
http://eawag-bbd.ethz.ch/predict/
The Pathway Prediction System (PPS) is linked to from the BBD and uses metabolic rules to predict plausible metabolic pathways by which chemical compounds might be biodegraded by microorganisms.
RAPID
The RAPID database and tool provides information on enzyme catalysis, and there is developing tool provided that is focused on identifying substrate‐enzyme compatibilities.
BRENDA
https://www.brenda-enzymes.org
BRENDA is an enzyme information system. It covers sources, substrates, inhibitors, kinetics and other characteristic features of the enzymes.
BioCyc
Bio/Cyc is an umbrella for different databases focused on metabolic pathways and genomes. It can be used to look at specific biocatalysis reactions or can be focused on the metabolism of specific microorganisms.
Biocatalysis chemistry database: Accelrys
http://accelrys.com/products/datasheets/biocatalysis.pdf
This is a commercial database that is focused on the use of enzymes and microorganisms for chemical synthesis, which might offer advantages of selectivity, efficiency and greater environmental friendliness.
EnviPath
EnviPath is a database that focuses on microbial degradation of organic chemicals in the environment.
EMBL biocatalysis links
http://identifiers.org/registry?query=enzyme
This page created by the European Bioinformatics Institute contains numerous links to sites and databases relevant to biocatalysis.
KEGG Ligand
http://www.genome.jp/kegg/kegg.html
The KEGG databases cover many aspects of cell function. It has extensive coverage of biochemical reactions, genes and enzyme nomenclature.
Catalytic site atlas
http://www.ebi.ac.uk/thornton-srv/databases/CSA/
The catalytic site atlas compiles information on enzyme active sites and catalytic residues as derived from the X‐ray structures of enzymes.
ExplorEnz database
http://www.enzyme-database.org
This enzyme database is organized along the lines of the Enzyme Commission classification system of enzyme reaction types.
Peroxibase
http://peroxibase.toulouse.inra.fr
Peroxidases are useful enzymes and this website focuses on peroxidase enzymes, both their sequences and their reactions.
CAZy:Carbohydrate‐active enzymes database
There are many commercially‐relevant reactions with carbohydrates and this database is dedicated to information on carbohydrate‐active enzymes.
Biocatalytic synthesis links
http://biocatalysis.uni-graz.at/sites/links.html
This page contains numerous links to sites on chemistry and biochemistry that is relevant to biocatalysis.
BioCatNet
The BioCatNet is a site that contains links to a collection of family‐specific enzyme databases, with a focus on enzymes of interest for biocatalysis.
PDB
The Protein DataBank (PDB) is a major resource for information on protein structures, typically determined by X‐ray crystallography or NMR methods.
PDBsum
http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=index.html
PDBsum is a pictorial database providing a visual overview of material from the PDB, showing protein, ligands, metals, etc.
Lipase database
http://www.au-kbc.org/beta/bioproj2/
Lipases have proven to be very versatile on the synthesis and chiral resolution of molecules, particularly in the pharmaceutical industry. This database focuses on information pertaining to lipases.
Pfam database
The Pfam database focuses on protein sequences within large protein families. It represents the data using multiple sequence alignments and hidden Markov models.
Cytochrome P450 engineering database
Cytochrome P450 enzymes are highly versatile because of their broad specificity and engineerability. This site focuses on a broad range of cytochrome P450 enzymes.
Microbial Biotechnology (2018) 11(2), 429–430