{"action":"created","issue":{"url":"https://api.github.com/repos/choderalab/dispensing-errors-manuscript/issues/17","labels_url":"https://api.github.com/repos/choderalab/dispensing-errors-manuscript/issues/17/labels{/name}","comments_url":"https://api.github.com/repos/choderalab/dispensing-errors-manuscript/issues/17/comments","events_url":"https://api.github.com/repos/choderalab/dispensing-errors-manuscript/issues/17/events","html_url":"https://github.com/choderalab/dispensing-errors-manuscript/issues/17","id":107958602,"number":17,"title":"IC50 vs. Ki?","user":{"login":"sonyahanson","id":6333823,"avatar_url":"https://avatars.githubusercontent.com/u/6333823?v=3","gravatar_id":"","url":"https://api.github.com/users/sonyahanson","html_url":"https://github.com/sonyahanson","followers_url":"https://api.github.com/users/sonyahanson/followers","following_url":"https://api.github.com/users/sonyahanson/following{/other_user}","gists_url":"https://api.github.com/users/sonyahanson/gists{/gist_id}","starred_url":"https://api.github.com/users/sonyahanson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sonyahanson/subscriptions","organizations_url":"https://api.github.com/users/sonyahanson/orgs","repos_url":"https://api.github.com/users/sonyahanson/repos","events_url":"https://api.github.com/users/sonyahanson/events{/privacy}","received_events_url":"https://api.github.com/users/sonyahanson/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":12,"created_at":"2015-09-23T16:34:44Z","updated_at":"2015-10-06T00:25:35Z","closed_at":null,"body":"Just wanted to double check. I'm not totally clear on how `scipy.optimize.curve_fit` works, but it seems like this function is actually fitting Ki and not IC50? \r\n\r\n<pre>\r\ndef fit_ic50(inhibitor_concentrations, activities):\r\n    def objective(inhibitor_concentrations, Ki):\r\n        activities = np.zeros([ndilutions], np.float64)\r\n        for i in range(ndilutions):\r\n            activities[i] = competitive_inhibition(substrate_concentration, inhibitor_concentrations[i], enzyme_concentration, Ki, Km)\r\n        return activities\r\n            \r\n    Ki_guess = true_Ki\r\n    import scipy.optimize\r\n    [popt, pcov] = scipy.optimize.curve_fit(objective, inhibitor_concentrations, activities, p0=[Ki_guess])\r\n    \r\n    return popt[0]\r\n</pre>\r\n\r\nLet me know if I'm mistaken here. I would think to fit Ki we would actually want to use the equation `IC50 = Ki* (1 + substrate_concentration/Km)` somewhere.\r\n\r\nI guess it is only different by a constant, so it is not a big deal, but i just want to make sure I'm not missing something."},"comment":{"url":"https://api.github.com/repos/choderalab/dispensing-errors-manuscript/issues/comments/145705603","html_url":"https://github.com/choderalab/dispensing-errors-manuscript/issues/17#issuecomment-145705603","issue_url":"https://api.github.com/repos/choderalab/dispensing-errors-manuscript/issues/17","id":145705603,"user":{"login":"sonyahanson","id":6333823,"avatar_url":"https://avatars.githubusercontent.com/u/6333823?v=3","gravatar_id":"","url":"https://api.github.com/users/sonyahanson","html_url":"https://github.com/sonyahanson","followers_url":"https://api.github.com/users/sonyahanson/followers","following_url":"https://api.github.com/users/sonyahanson/following{/other_user}","gists_url":"https://api.github.com/users/sonyahanson/gists{/gist_id}","starred_url":"https://api.github.com/users/sonyahanson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sonyahanson/subscriptions","organizations_url":"https://api.github.com/users/sonyahanson/orgs","repos_url":"https://api.github.com/users/sonyahanson/repos","events_url":"https://api.github.com/users/sonyahanson/events{/privacy}","received_events_url":"https://api.github.com/users/sonyahanson/received_events","type":"User","site_admin":false},"created_at":"2015-10-06T00:25:35Z","updated_at":"2015-10-06T00:25:35Z","body":"This doesn't seem to have changed anything. I did change the fit to be fitting to IC50, instead of Ki, it is rather hacky."}}