{"id":7574,"date":"2021-11-09T15:58:47","date_gmt":"2021-11-09T15:58:47","guid":{"rendered":"https:\/\/www.blopig.com\/blog\/?p=7574"},"modified":"2021-11-09T15:58:49","modified_gmt":"2021-11-09T15:58:49","slug":"using-normalized-sucos-scores","status":"publish","type":"post","link":"https:\/\/www.blopig.com\/blog\/2021\/11\/using-normalized-sucos-scores\/","title":{"rendered":"Using normalized SuCOS scores."},"content":{"rendered":"\n

If you are working in cheminformatics or utilise protein-ligand docking, then you should be aware of the SuCOS score, an open-source shape and chemical feature overlap metric<\/a> designed by a former member of OPIG: Susan Leung.

The metric compares the 3D conformers of two ligands based on their shape overlap as well as their chemical feature overlap using the RDKit<\/a> toolkit. Leung et al.<\/em><\/a> <\/em>show that SuCOS is able to select fewer false positives and false negatives when doing re-docking studies than other scoring metrics such as RMSD or Protein Ligand Interaction Fingerprints (PLIF) similarity scores and performs better at differentiating actives from decoys when tested on the DUD-E dataset.

Most importantly, SuCOS was designed with fragment based drug discovery in focus, where a smaller fragment ligand is elaborated or combined with other fragments to create a larger molecule, with hopefully stronger binding affinity. Unlike for example RMSD, SuCOS is able to quickly calculate an overlap score between a small fragment and a larger molecule, giving chemists an idea on how the fragment elaboration might interact with the protein. However, the original SuCOS algorithm<\/a> was not normalized and could create scores of > 1 for some cases. <\/p>\n\n\n\n

I’ve uploaded a normalised version of the original SuCOS algorithm as a GitHub fork of Susan’s original repository. You can find the normalised SuCOS algorithm here.<\/a><\/p>\n\n\n\n

Hopefully this is helpful for anyone using the SuCOS algorithm and for all docking enthusiasts who are interested in an alternative way to evaluate their docked poses. <\/p>\n","protected":false},"excerpt":{"rendered":"

If you are working in cheminformatics or utilise protein-ligand docking, then you should be aware of the SuCOS score, an open-source shape and chemical feature overlap metric designed by a former member of OPIG: Susan Leung. The metric compares the 3D conformers of two ligands based on their shape overlap as well as their chemical […]<\/p>\n","protected":false},"author":62,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"nf_dc_page":"","wikipediapreview_detectlinks":true,"_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"ngg_post_thumbnail":0,"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[187,29,291,227],"tags":[],"ppma_author":[543],"class_list":["post-7574","post","type-post","status-publish","format-standard","hentry","category-cheminformatics","category-code","category-protein-ligand-docking","category-python-code"],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"authors":[{"term_id":543,"user_id":62,"is_guest":0,"slug":"marc","display_name":"Marc M\u00f6\u00dfer (Moesser)","avatar_url":"https:\/\/secure.gravatar.com\/avatar\/08164edbfa69b99d7ddb64e2d18e0b76cfd59ce4ade51ffbe2abd72aa5419f7e?s=96&d=mm&r=g","0":null,"1":"","2":"","3":"","4":"","5":"","6":"","7":"","8":""}],"_links":{"self":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/7574","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/users\/62"}],"replies":[{"embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/comments?post=7574"}],"version-history":[{"count":3,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/7574\/revisions"}],"predecessor-version":[{"id":7578,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/7574\/revisions\/7578"}],"wp:attachment":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/media?parent=7574"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/categories?post=7574"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/tags?post=7574"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/ppma_author?post=7574"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}