Skip to main content

Table 1 Summary of available settings and options for fine-tuning the sugar detection and removal in the SRU, along with their impact, default, and availability

From: Too sweet: cheminformatics for deglycosylation in natural products

Setting Options Impact on Default Availability
Type of sugar moieties to remove Circular/linear/both Sugar removal (None) Web application, command-line application, source code
Remove only terminal sugars Yes/no Sugar removal Yes Web application, command-line application, source code
Preservation mode Preserve all/judge by heavy atoms / judge by molecular weight Sugar removal Judge by heavy atoms Command-line application, source code
Preservation mode threshold Any number of heavy atoms or a molecular weight ≥ 0 Sugar removal 5 heavy atoms Command-line application, source code
Detect circular sugars only with O-glycosidic bond Yes/no Circular sugar detection (and removal) No Web application, command-line application, source code
Detect circular sugars only with enough exocyclic oxygen atoms Yes/no Circular sugar detection (and removal) Yes Command-line application, source code
Exocyclic oxygen atoms to atoms in ring ratio threshold Any ratio ≥ 0 Circular sugar detection (and removal) 0.5 (five- and six-membered sugar rings need at least 3 connected oxygen atoms) Command-line application, source code
Detect spiro rings as circular sugars Yes/no Circular sugar detection (and removal) No Command-line application, source code
Detect linear sugars in rings Yes/no Linear sugar detection (and removal) No Command-line application, source code
Linear sugar candidate minimum size Any number of carbon atoms ≥ 1 Linear sugar detection (and removal) 4 carbon atoms Command-line application, source code
Linear sugar candidate maximum size Any number of carbon atoms ≥ 1 Linear sugar detection (and removal) 7 carbon atoms Command-line application, source code
Detect linear acidic sugars Yes/no Linear sugar detection (and removal) No Command-line application, source code
Circular/linear sugar patterns Adding/removing patterns Circular/linear sugar detection (and removal) Pre-compiled set of circular and linear sugars (see Figs. 5 and 6) Source code