Psicquic channels: Difference between revisions
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= Target-Target Channels = | = Target-Target Channels (tt) = | ||
* 1. Sea prediction (T-T) | * 1. Sea prediction (T-T) (swissprot to swissprot) | ||
* 2. blast similarity (Evalue) | * 2. blast similarity (Evalue) | ||
* 3. co-expression data from Matt (100 to 0 percentile rank) | * 3. co-expression data from Matt (100 to 0 percentile rank) | ||
| Line 6: | Line 6: | ||
* 5. PPI (biogrid, experimental) | * 5. PPI (biogrid, experimental) | ||
= Target-Compound Channels = | = Target-Compound Channels (ct) = | ||
* 1. Experimental binder, is bioactive and binds 1uM or better per chembl20 | * 1. Experimental binder, is bioactive and binds 1uM or better per chembl20 (chebi name to swissprot name) | ||
* 2. is a drug and binds target 10uM or better | * 2. is a drug and binds target 10uM or better | ||
* 3. Is biogenic and binding 1uM or better | * 3. Is biogenic and binding 1uM or better | ||
* 4. is and endogenous metabolite for this target | * 4. is and endogenous metabolite for this target | ||
* 5. SEA prediction (TC, P-value) | * 5. SEA prediction (TC, P-value) (chebi to swissprot) | ||
= Compound-Compound Channels (cc) | |||
* 1. EBI compound (chebi) to ZINC (zincid) | |||
* 2. nearest metabolite, drug, biogenic, purchasable | |||
* NB not supported at our client, but we can still prepare for it | |||
= how to restart the server = | |||
* become root on zeta | |||
* create screen and su to psicquic | |||
* cd psicquic-solr-ws-1.3.14 (or latest) | |||
* bash startPsicquicServerAndSolr.sh /home/psicquic/solr11 ( to start server) | |||
* optional: to rebuild data: bash indexMitab.sh /home/psicquic/channel2a.txt /home/psicquic/solr/ | |||
Latest revision as of 23:31, 30 January 2018
Target-Target Channels (tt)
- 1. Sea prediction (T-T) (swissprot to swissprot)
- 2. blast similarity (Evalue)
- 3. co-expression data from Matt (100 to 0 percentile rank)
- 4. shared ligand, 1uM or better
- 5. PPI (biogrid, experimental)
Target-Compound Channels (ct)
- 1. Experimental binder, is bioactive and binds 1uM or better per chembl20 (chebi name to swissprot name)
- 2. is a drug and binds target 10uM or better
- 3. Is biogenic and binding 1uM or better
- 4. is and endogenous metabolite for this target
- 5. SEA prediction (TC, P-value) (chebi to swissprot)
= Compound-Compound Channels (cc)
- 1. EBI compound (chebi) to ZINC (zincid)
- 2. nearest metabolite, drug, biogenic, purchasable
- NB not supported at our client, but we can still prepare for it
how to restart the server
- become root on zeta
- create screen and su to psicquic
- cd psicquic-solr-ws-1.3.14 (or latest)
- bash startPsicquicServerAndSolr.sh /home/psicquic/solr11 ( to start server)
- optional: to rebuild data: bash indexMitab.sh /home/psicquic/channel2a.txt /home/psicquic/solr/