Tool-selector

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This page describes the tool selector. It is password protected, thus only for members of the lab.


version 1

Here is a brief introduction to the tool compound editor.


  • step 1. go to the tool compound website (ask John)
  • genes listed in alpha order down LHS
  • selected tool compounds shown on right.
  • numbers are # orthogonal sets of eligible compounds. then number of purchsasble compounds
  • step 2. click on a gene to get the gene detail view on the right
  • box shows currently selected compounds.
  • compounds can be promoted/demoted using the + (-) in the top right corner of the molecule displayed during hover
  • below each compound we show affinity for this target, affinity for next best target (which can be higher), and purchasability (50=premier vendor, 40=in stock vendor, 30 = agent (e.g. emolecules), 20 = on demand, 10 = boutique (likely expensive) 1 = not for sale
  • if compound is fda approved, world drug, investigational ,etc, this is shown .
  • zincid is clickable and takes you to zinc where more info is displayed
  • changes only saved when save button (top right) is pressed.
  • "eject" button takes you back to listing view
  • next takes you to next page. Also just edit URL to jump ahead to other pages.
  • there are some weird display bugs (sometimes you need to ctrl-shift load to force a cache refresh. We are aware and are working on this.
  • please comment directly to JJI (bugs, feature requests, poor choices, suggestions, etc)

version 2

Click Next (top left) to go to the next page, or edit the URL to jump to a later page: e.g.

http://tool-selector.ucsf.bkslab.org/#/genes?page=20 

40 pages, 50 genes per page.

Suggest you do :

http://tool-selector.ucsf.bkslab.org/#/genes?page=35

but choose any page you like.

Each line is as follows:

Gene symbol. Click it to go to the detail page
second column: number of compounds annotated in ChEMBL20, number of tool compounds selected.
third column: selected tool compounds (click to view in ZINC)

click on gene symbol to go to the detail page for that gene.

box at top: tool compounds chosen.
left: navigate to other genes.
lower right: pool of compounds to select from

you can promote or demote tool compounds. you must click save (top right green button) to commit your changes.

You must click on save to save the comments separately.


Please let me know when you've had a chance to review 10 cmps so we can talk.


Curator's section

Here is how to refresh the purchasability of the observations

curl http://zinc15.docking.org/observations.txt -F count=all -F distinct=no -F sort=no -F substance.purchasable-gt=1 \
-F output_fields="substance.inchikey_prefix gene_name affinity ortholog.name zinc_id substance.features substance.purchasable substance.ecfp4_new.base64"  > newobs.xls

Then sort, filter, add header, restart server.