{"action":"created","issue":{"url":"https://api.github.com/repos/eppic-team/eppic/issues/6","repository_url":"https://api.github.com/repos/eppic-team/eppic","labels_url":"https://api.github.com/repos/eppic-team/eppic/issues/6/labels{/name}","comments_url":"https://api.github.com/repos/eppic-team/eppic/issues/6/comments","events_url":"https://api.github.com/repos/eppic-team/eppic/issues/6/events","html_url":"https://github.com/eppic-team/eppic/issues/6","id":47131276,"number":6,"title":"MHC to peptide complexes: problems in core-surface scoring","user":{"login":"josemduarte","id":6000474,"avatar_url":"https://avatars.githubusercontent.com/u/6000474?v=3","gravatar_id":"","url":"https://api.github.com/users/josemduarte","html_url":"https://github.com/josemduarte","followers_url":"https://api.github.com/users/josemduarte/followers","following_url":"https://api.github.com/users/josemduarte/following{/other_user}","gists_url":"https://api.github.com/users/josemduarte/gists{/gist_id}","starred_url":"https://api.github.com/users/josemduarte/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/josemduarte/subscriptions","organizations_url":"https://api.github.com/users/josemduarte/orgs","repos_url":"https://api.github.com/users/josemduarte/repos","events_url":"https://api.github.com/users/josemduarte/events{/privacy}","received_events_url":"https://api.github.com/users/josemduarte/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2014-10-29T10:24:24Z","updated_at":"2016-11-08T16:50:58Z","closed_at":"2016-11-08T16:50:58Z","body":"<a href=\"https://github.com/josemduarte\"><img src=\"https://avatars.githubusercontent.com/u/6000474?v=2\" align=\"left\" width=\"96\" height=\"96\" hspace=\"10\"></img></a> **Issue by [josemduarte](https://github.com/josemduarte)**\n_Monday Jun 23, 2014 at 10:42 GMT_\n_Originally opened as https://github.com/eppic-team/eppic-cli/issues/10_\n---\n\nIn MHC-to-peptide complexes (e.g. 1w0w) the protein side gives usually a very high (xtal) score because the actual site that binds the peptide is the most variable in terms of sequence, this is an issue similar to antibodies. The difference is that for antibodies usually there's quite a mismatch from the PDB sequence to the found UniProt reference and then a nopred is produced because all the mismatches. For some reason in MHC case the found UniProt reference is usually matching very well and then the prediction procedes as usual. If one looks at the potato for one of these cases it's almost a negative of the usual situation: the binding site is warm colors and the rest of the surface is blue. \n\nE.g. for 1w0w one gets a core-surface score of 11.84\n\nSee also issue #9 which tends to happen together with this one as the partners of the MHC are always peptides\n"},"comment":{"url":"https://api.github.com/repos/eppic-team/eppic/issues/comments/259191883","html_url":"https://github.com/eppic-team/eppic/issues/6#issuecomment-259191883","issue_url":"https://api.github.com/repos/eppic-team/eppic/issues/6","id":259191883,"user":{"login":"sbliven","id":595872,"avatar_url":"https://avatars.githubusercontent.com/u/595872?v=3","gravatar_id":"","url":"https://api.github.com/users/sbliven","html_url":"https://github.com/sbliven","followers_url":"https://api.github.com/users/sbliven/followers","following_url":"https://api.github.com/users/sbliven/following{/other_user}","gists_url":"https://api.github.com/users/sbliven/gists{/gist_id}","starred_url":"https://api.github.com/users/sbliven/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sbliven/subscriptions","organizations_url":"https://api.github.com/users/sbliven/orgs","repos_url":"https://api.github.com/users/sbliven/repos","events_url":"https://api.github.com/users/sbliven/events{/privacy}","received_events_url":"https://api.github.com/users/sbliven/received_events","type":"User","site_admin":false},"created_at":"2016-11-08T16:50:58Z","updated_at":"2016-11-08T16:50:58Z","body":"Some false negatives are acceptable. I think we're doing the best we can."}}
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