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bindingdb.org scraper Target/Host, species, KinM, IC50nM, kd nm, EC50nM with sorting and delete non human study if human study is available, and what that value means plus koff s-1, Kon, Emax/ imax

 what is bindingdb.org scraper:

bindingdb.org is a meta search engine that fetch data from other search engine like PSPP,
i tried to find a easy way to know the median binding of a substance using bindingdb.org but the data was hard to use , so i developed a script that will scrap the data and give you easy way to know the median binding of any substance

change log:
v0.5
-fix rare case where the script can't fetch all results in one time
-better javascript codes with the same function
v0.4
-fix "delete non human study if human study is available for specific receptor" button not working after sorting the table
-add link to check update for this script
v0.3
-fix the button "click here to start fetching data and wait.." don't work when the substance has less then 50 result
v0.2
-better style in some browsers
v0.1
-first version
-table sorting when click on first table row, you can sort alphabetically by Target/Host, species, KinM, IC50nM, kd nm, EC50nM
-give alert when data was not fully loaded
-set a link to fetch all data instead of 50 everytime
-delete non human study if human study is available

how to use:

 
note: tampermonkey android app doesn't work, and tampermonkey addon for firefox android is not available as of 2021-8-4, as for android chrome users, if you can install tampermonkey or any userscript manager it will works, test it and give us a feedback :)

 then click here to install the userscript (if tampermonkey did not detect it then copy it's content and choose create new script and put it there)

now after installing open advanced search page of bindingdb.org by clicking here
(sometimes the service is down due to maintenance or capacity problems)
 
you will see like this
choose compound name
and type substance name and choose exact, the click "run search"



then in next page click "click here to start fetching data and wait.."



then in next page click "delete non human study if human study is available for specific receptor"

now click on Target/Host to sort the table using that

and then copy the content

Ki nM= mean how well the substance can bind to a receptor =the lower the better

IC50 = Half-maximal inhibitory concentration =the lower the better= i do believe its always mean antagonist

EC50= Half maximal effective concentration=the lower the better= i do believe its always mean agonist

Kd nM =The equilibrium dissociation constant. represents the concentration of radioligand. occupying half of the maximum receptor. =the lower the better=its mean the how well the drug can bind to receptor (like ki nm)

koff s-1=A higher value for Koff means a shorter lifetime for the complex and vice versa=the lower the better=not important in drug potency, ki and other have the real rule koff can be weak and the drug be strong, KD is computed from Koff/Kon

Kon =the lower the better=is the association constant in inverse minutes multiplied by inverse concentration, not important in drug potency, ki and other have the real rule koff can be weak and the drug be strong

Emax/ imax=efficacy= the higher the better= its not available in bindingdb.org


go to excel and past that content, you will have something like this

select receptor Ki nM like this


in bottom corner of excel you will see the median Ki value for that target


note: because bindingdb.org use many names for the same target like
Norepinephrine transporter
Sodium-dependent noradrenaline transporter
 
the "delete non human study if human study is available for specific receptor" function can't delete all target, so you need to do it in excel, the function will just make it easier

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