Frequently Asked Question

Q: How does RAPID predict substrates?

A: The current version of the algrorithm used to predict oxygenase substrates can be found at:
Escalante, D. E., Aukema, K. G., Wackett, L. P., & Aksan, A. (2017). Simulation of the Bottleneck Controlling Access into a Rieske Active Site: Predicting Substrates of Naphthalene 1, 2-Dioxygenase. J. Chem. Inf. Model57(3), 550-561.

And the first succesful application of the algorithm can be found at:
Aukema, K. G., Escalante, D. E., Maltby, M. M., Bera, A. K., Aksan, A., & Wackett, L. P. (2016). In Silico Identification of Bioremediation Potential: Carbamazepine and Other Recalcitrant Personal Care Products. Environmental science & technology51(2), 880-888.


Q: Will RAPID cover all enzymes?

A: No, unlike some databases that seek to cover enzymes comprehensively, RAPID is based on the premise that there are a small number of enzymes with very broad-substrate specificity that are most useful in biocatalysis.


Q: How many substrates will RAPID cover?

A: As many as are known, or can be predicted. Some of the enzymes on RAPID have hundreds of known substrates. Predicted substrates may extend to more than 10,000.


Q: What compounds are in RAPID?

A: RAPID compounds are documented substrates, products or non-substrates of RAPID enzymes.  Non-substrates include inhibitors.  To report omissions or corrections, please email


Q: How is RAPID information documented?

A: Information on enzymes, their substrates and products, and their non-substrates, comes from articles in the peer-reviewed scientific literature.  Secure links to these articles are to the journal’s website through PubMed abstracts (PMIDs, ) or, when PMIDs are not available, Digital Object Identifiers (DOIs, ).  When more than one article is available, presently only one link used.  As time permits, links to the other articles will be added. 


Q: What are the important sources of information for RAPID enzyme and compound pages?

A: On an enzyme page, the structures come from the Research Collaboratory for Structional Biology Protein Data Bank (PDB) ( ).  An entry is identified by its PDB ID.  On a compound page, the list of synonyms comes from the NIH Cactus database ( ).  We thank the sponsors and maintainers of these valuable databases.