http://rest.genome.jp/simcomp/<query>/<database>[/<params>]
<query> = KEGG COMPOUND/DRUG or KNApSAcK entry ID
<database> = compound (default) | drug | knapsack | reaction |
KEGG COMPOUND/DRUG or KNApSAcK entry IDs
<params> = <param>[/<params>]
<param> = offset=<num> | limit=<num> | cutoff=<num> | dnode=[0|2] | atom=[0|1|2] |
trick=[0|2|none] | trickatom=[0|1|2] | mode=[local|global] | chiral=[on|off] |
kcfoutput=[on|off]
|
| /simcomp/C00022 | searches compounds similar to KEGG C00022 (pyruvate) from KEGG COMPOUND | |||
| /simcomp/C00022/C00186+C00256+C01432+C00109+C00957/mode=local | ||||
| searches compounds similar to KEGG C00022 from five compounds in KEGG COMPOUND using the local search mode | ||||
| /simcomp/C00022/compound/cutoff=0.6/dnode=2/atom=2/trick=2/trickatom=0/limit=10/chiral=off | ||||
| searches compounds similar to KEGG C00022 from KEGG COMPOUND using the specified parameters | ||||
| /simcomp/C00022/knapsack/kcfoutput=on | ||||
| searches compounds similar to KEGG C00022 (pyruvate) from KNApSAcK with KCF alignment outputs. | ||||
| Use command line tools such as curl | ||||
| % curl -F molfile=@<filename> http://rest.genome.jp/simcomp/ | ||||
| % curl -F kcffile=@<filename> http://rest.genome.jp/simcomp/ | ||||
| % curl -F smiles='O=C(C(=O)O)C' -F cutoff=0.6 -F limit=10 http://rest.genome.jp/simcomp/ | ||||
| offset: | Number for starting index, e.g. 11 for showing results from the 11th hit |
| limit: | Number of hits shown from the top or the index specified by offset |
| cutoff: | Threshold score; default=0.4 |
| dnode: | Docking mode; 0: Atom based; 2: Bond based (default) |
| atom: | Docking atom; 0: Atom species; 1: Atom class; 2: KEGG atom (default) |
| trick: | Enable post-processing; 0: for the largest SCCS; 2: for all SCCSs (default); none: disable post-processing |
| trickatom: | Docking atom for post-processing; 0: Atom species (default); 1: Atom class; 2: KEGG atom |
| mode: | local: same as dnode=2, atom=2, trick=0 and trickatom=1 |
| global: same as dnode=2, atom=2, trick=2 and trickatom=0 | |
| chiral: | on: enable chiral check (default); off: disable chiral check |
| kcfoutput: | on: enable KCF alignment output; off: output IDs and socres only (default) |
http://rest.genome.jp/simcomp2/<query1>/<query2>[/<params>]
<query1> = <query2> = KEGG COMPOUND/DRUG or KNApSAcK entry IDs
<params> = <param>[/<params>]
<param> = offset=<num> | limit=<num> | cutoff=<num> | dnode=[0|2] | atom=[0|1|2] |
trick=[0|2|none] | trickatom=[0|1|2] | mode=[local|global] | chiral=[on|off] |
kcfoutput=[on|off]
|
| /simcomp2/C00022/C00186 | calculate similarity between KEGG C00022 (pyruvate) and C00186 (S-Lactate) | |||
| /simcomp2/C00022+C00186/C00256+C01432+C00109+C00957/mode=local | ||||
| calculate all to all similarities between the first and second sets using the local search mode | ||||
| /simcomp2/C00022+C00186/C00256+C01432+C00109+C00957/cutoff=0.6/dnode=2/atom=2/trick=2/trickatom=0/limit=10/chiral=off | ||||
| calculate all to all similarities between the first and second sets using the specified parameters | ||||
| /simcomp2/C00022+C00186/C00256+C01432+C00109+C00957/kcfoutput=on | ||||
| calculate all to all similarities between the first and second sets, and output with KCF alignment format | ||||
| Use command line tools such as curl | ||||
| % curl -F query_file=@<queryfilename> -F target_file=@<targetfilename> http://rest.genome.jp/simcomp2/ | ||||
| Input files should be single files in the SDF or concatenated MOL format. | ||||
| Same as simcomp other than the cutoff default is 0.8 |
http://rest.genome.jp/subcomp/<query>/<database>[/<params>]
<query> = KEGG COMPOUND/DRUG or KNApSAcK entry ID
<database> = compound (default) | drug | knapsack | reaction |
KEGG COMPOUND entry IDs
<params> = <param>[/<params>]
<param> = offset=<num> | limit=<num> | cutoff=<num> | mode=[all|sub|sup] | charge=[on|off] |
valence=[on|off] | coordinate=[on|off] | chiral=[on|off] | kcfoutput=[on|off]
|
| /subcomp/C00022 | searches substructures for KEGG C00022 (pyruvate) from KEGG COMPOUND | |||
| /subcomp/C00022/C00048+C00141+C17265+C00109+C00957/mode=sup | ||||
| searches superstructures for KEGG C00022 from five compounds in KEGG COMPOUND | ||||
| /subcomp/C00022/compound/cutoff=0.6/limit=10/mode=all/charge=on/coordinate=on/valence=on/chiral=on | ||||
| searches substructures for KEGG C00022 from KEGG COMPOUND using the specified parameters | ||||
| /subcomp/C00022/C00048+C00141+C17265+C00109+C00957/kcfoutput=on | ||||
| searches sub/superstructures for KEGG C00022 from five compounds in KEGG COMPOUND with KCF alignment outputs | ||||
| Use command line tools such as curl | ||||
| % curl -F molfile=@<filename> http://rest.genome.jp/subcomp/ | ||||
| % curl -F kcffile=@<filename> http://rest.genome.jp/subcomp/ | ||||
| % curl -F smiles='O=C(C(=O)O)C' -F cutoff=0.8 -F limit=10 http://rest.genome.jp/subcomp/ | ||||
| offset: | Number for starting index, e.g. 11 for showing results from the 11th hit |
| limit: | Number of hits shown from the top or the index specified by offset |
| cutoff: | Threshold score; default=0 |
| mode: | Search mode; all: all matches (default); sub: only substructures; sup: only superstructures |
| charge: | Distinguish charged atom, e.g. "OH" from "O-"; default is off |
| valence: | Distinguish valence, e.g. "S<" from "=S="; default is off |
| coordinate: | Consider coordinate bond, e.g. "[X+]-[Y-]" as "X=Y"; default is off |
| chiral: | on: enable chiral check; off: disable chiral check (default) |
http://rest.genome.jp/mol2kcf/ This operation only allows file uploads |
| Use command line tools such as curl | ||||
| % curl -F molfile=@<filename> http://rest.genome.jp/mol2kcf/ | ||||