{"id":196,"date":"2020-10-23T11:00:21","date_gmt":"2020-10-23T11:00:21","guid":{"rendered":"http:\/\/www.ebi.ac.uk\/training\/online\/courses\/structural-volume-data\/scoring-functions-of-volume-matching\/"},"modified":"2020-10-23T11:01:46","modified_gmt":"2020-10-23T11:01:46","slug":"scoring-functions-of-volume-matching","status":"publish","type":"page","link":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/structural-volume-data\/scoring-functions-of-volume-matching\/","title":{"rendered":"Scoring functions of volume matching"},"content":{"rendered":"\n<p class=\"wp-block-paragraph\">Volume matching algorithms yield a set of putative alignments between a pair of volumes. These are typically scored according to some criterion internal to the software used. However, there are a range of scoring functions which can be applied to get external validation, and these can be sensitive to different characteristics of the volumes. If there is a consensus between several different scores, then one can have some confidence in the proposed alignment.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Several scoring functions have been designed for quantifying the quality of alignments. A comparison is available of these functions in the Vasishtan and Topf (2011) review paper:<\/p>\n\n\n\n<ol class=\"wp-block-list\"><li>Local Cross-Correlation Coefficient (Roseman AM. 2000) &#8211; a correlation coefficient between the density values of the two maps, calculated for the overlap region only<\/li><li>Laplacian-filtered CCF (Chacon and Wriggers, 2002) &#8211; the Laplacian filter helps to pick out the surfaces of the volumes<\/li><li>Overlap score (Chimera, Pettersen et al. 2004) &#8211; fraction of overlapping voxels with respect to the smaller of the two volumes<\/li><li>Core-weighted envelope score (Wu et al. 2003) &#8211; a cumulative measure based on the number of overlapping voxels, with a penalty for non-overlapping voxels<\/li><li>Mutual information score (Shatsky et al. 2009) &#8211; a measure of how similar the joint distribution of density values in the superimposed maps is to the individual density distributions<\/li><li>Chamfer distance (Knossow et al. 2008) &#8211; an average distance between nearest neighbour points on the surfaces of the two superimposed maps.<\/li><li>Normal Vector score (Ceulemans and Russell. 2004) &#8211; an average angle between vectors normal to the two surfaces<\/li><\/ol>\n\n\n\n<p class=\"wp-block-paragraph\">Many of these scoring functions depend on the surface of the volume being identified as a particular contour level of the map. The choice of contour level is not necessarily straightforward.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Volume matching algorithms yield a set of putative alignments between a pair of volumes. These are typically scored according to some criterion internal to the software used. However, there are a range of scoring functions which can be applied to get external validation, and these can be sensitive to different characteristics of the volumes. If&#8230;<\/p>\n","protected":false},"author":30,"featured_media":0,"parent":0,"menu_order":5,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-196","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/structural-volume-data\/wp-json\/wp\/v2\/pages\/196","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/structural-volume-data\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/structural-volume-data\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/structural-volume-data\/wp-json\/wp\/v2\/users\/30"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/structural-volume-data\/wp-json\/wp\/v2\/comments?post=196"}],"version-history":[{"count":1,"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/structural-volume-data\/wp-json\/wp\/v2\/pages\/196\/revisions"}],"predecessor-version":[{"id":204,"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/structural-volume-data\/wp-json\/wp\/v2\/pages\/196\/revisions\/204"}],"wp:attachment":[{"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/structural-volume-data\/wp-json\/wp\/v2\/media?parent=196"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}