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. Model, 57(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 & technology, 51(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 firstname.lastname@example.org.
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, https://pubmed.gov/ ) or, when PMIDs are not available, Digital Object Identifiers (DOIs, https://doi.org/ ). 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) (http://rcsb.org/ ). An entry is identified by its PDB ID. On a compound page, the list of synonyms comes from the NIH Cactus database (https://cactus.nci.nih.gov/chemical/structure ). We thank the sponsors and maintainers of these valuable databases.