{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,27]],"date-time":"2026-09-27T09:37:24Z","timestamp":1790501844331,"version":"4.1.0"},"reference-count":44,"publisher":"Wiley","issue":"6","license":[{"start":{"date-parts":[[2018,4,27]],"date-time":"2018-04-27T00:00:00Z","timestamp":1524787200000},"content-version":"am","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2018,4,27]],"date-time":"2018-04-27T00:00:00Z","timestamp":1524787200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["MCB\u20101158176"],"award-info":[{"award-number":["MCB\u20101158176"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["CHE\u20101305655"],"award-info":[{"award-number":["CHE\u20101305655"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100001797","name":"Pharmaceutical Research and Manufacturers of America Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100001797","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000048","name":"American Cancer Society","doi-asserted-by":"publisher","award":["RSG\u201012\u2010161\u201001\u2010DMC"],"award-info":[{"award-number":["RSG\u201012\u2010161\u201001\u2010DMC"]}],"id":[{"id":"10.13039\/100000048","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000081","name":"Directorate for Education and Human Resources","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000081","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Protein Science"],"published-print":{"date-parts":[[2018,6]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>As a result of high\u2010throughput protein structure initiatives, over 14,400 protein structures have been solved by Structural Genomics (SG) centers and participating research groups. While the totality of SG data represents a tremendous contribution to genomics and structural biology, reliable functional information for these proteins is generally lacking. Better functional predictions for SG proteins will add substantial value to the structural information already obtained. Our method described herein, Graph Representation of Active Sites for Prediction of Function (GRASP\u2010Func), predicts quickly and accurately the biochemical function of proteins by representing residues at the predicted local active site as graphs rather than in Cartesian coordinates. We compare the GRASP\u2010Func method to our previously reported method, Structurally Aligned Local Sites of Activity (SALSA), using the Ribulose Phosphate Binding Barrel (RPBB), 6\u2010Hairpin Glycosidase (6\u2010HG), and Concanavalin A\u2010like Lectins\/Glucanase (CAL\/G) superfamilies as test cases. In each of the superfamilies, SALSA and the much faster method GRASP\u2010Func yield similar correct classification of previously characterized proteins, providing a validated benchmark for the new method. In addition, we analyzed SG proteins using our SALSA and GRASP\u2010Func methods to predict function. Forty\u2010one SG proteins in the RPBB superfamily, nine SG proteins in the 6\u2010HG superfamily, and one SG protein in the CAL\/G superfamily were successfully classified into one of the functional families in their respective superfamily by both methods. This improved, faster, validated computational method can yield more reliable predictions of function that can be used for a wide variety of applications by the community.<\/jats:p>","DOI":"10.1002\/pro.3416","type":"journal-article","created":{"date-parts":[[2018,3,31]],"date-time":"2018-03-31T15:24:40Z","timestamp":1522509880000},"page":"1125-1135","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Functional classification of protein structures by local structure matching in graph representation"],"prefix":"10.1002","volume":"27","author":[{"given":"Caitlyn L.","family":"Mills","sequence":"first","affiliation":[{"name":"Department of Chemistry and Chemical Biology Northeastern University Boston Massachusetts"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rohan","family":"Garg","sequence":"additional","affiliation":[{"name":"College of Computer and Information Science Northeastern University Boston Massachusetts"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joslynn S.","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Chemical Biology Northeastern University Boston Massachusetts"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liang","family":"Tian","sequence":"additional","affiliation":[{"name":"Department of Mathematics Northeastern University Boston Massachusetts"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexandru","family":"Suciu","sequence":"additional","affiliation":[{"name":"Department of Mathematics Northeastern University Boston Massachusetts"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gene D.","family":"Cooperman","sequence":"additional","affiliation":[{"name":"College of Computer and Information Science Northeastern University Boston Massachusetts"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7770-022X","authenticated-orcid":false,"given":"Penny J.","family":"Beuning","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Chemical Biology Northeastern University Boston Massachusetts"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mary Jo","family":"Ondrechen","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Chemical Biology Northeastern University Boston Massachusetts"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2018,4,27]]},"reference":[{"key":"e_1_2_5_2_1","doi-asserted-by":"publisher","DOI":"10.1093\/bfgp\/eln030"},{"key":"e_1_2_5_3_1","doi-asserted-by":"publisher","DOI":"10.1007\/978-94-007-0881-5"},{"key":"e_1_2_5_4_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00203-010-0549-9"},{"key":"e_1_2_5_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.csbj.2015.02.003"},{"key":"e_1_2_5_6_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrm2281"},{"key":"e_1_2_5_7_1","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2009-10-2-207"},{"key":"e_1_2_5_8_1","doi-asserted-by":"publisher","DOI":"10.1038\/msb4100129"},{"key":"e_1_2_5_9_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.sbi.2015.01.007"},{"key":"e_1_2_5_10_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ymeth.2015.11.010"},{"key":"e_1_2_5_11_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(02)00016-5"},{"key":"e_1_2_5_12_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2003.08.057"},{"key":"e_1_2_5_13_1","doi-asserted-by":"publisher","DOI":"10.1021\/bi201312u"},{"key":"e_1_2_5_14_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1000605"},{"key":"e_1_2_5_15_1","doi-asserted-by":"publisher","DOI":"10.1142\/S0219720010005166"},{"key":"e_1_2_5_16_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-14-S3-S13"},{"key":"e_1_2_5_17_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1000266"},{"key":"e_1_2_5_18_1","doi-asserted-by":"publisher","DOI":"10.1110\/ps.073213608"},{"key":"e_1_2_5_19_1","doi-asserted-by":"publisher","DOI":"10.1002\/bip.21589"},{"key":"e_1_2_5_20_1","doi-asserted-by":"publisher","DOI":"10.1002\/prot.23035"},{"key":"e_1_2_5_21_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(05)80134-2"},{"key":"e_1_2_5_22_1","doi-asserted-by":"publisher","DOI":"10.1515\/BC.2001.163"},{"key":"e_1_2_5_23_1","doi-asserted-by":"publisher","DOI":"10.1002\/pro.463"},{"key":"e_1_2_5_24_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0035-9203(08)70022-1"},{"key":"e_1_2_5_25_1","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00579-06"},{"key":"e_1_2_5_26_1","doi-asserted-by":"publisher","DOI":"10.1038\/msb.2011.75"},{"key":"e_1_2_5_27_1","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(92)90665-7"},{"key":"e_1_2_5_28_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(02)00378-9"},{"key":"e_1_2_5_29_1","doi-asserted-by":"publisher","DOI":"10.1021\/bi9907734"},{"key":"e_1_2_5_30_1","doi-asserted-by":"publisher","DOI":"10.1021\/bi026092h"},{"key":"e_1_2_5_31_1","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M102012200"},{"key":"e_1_2_5_32_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(02)01374-8"},{"key":"e_1_2_5_33_1","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1999.2643"},{"key":"e_1_2_5_34_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.259441296"},{"key":"e_1_2_5_35_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0959-440X(00)00148-2"},{"key":"e_1_2_5_36_1","doi-asserted-by":"publisher","DOI":"10.1002\/chem.200900397"},{"key":"e_1_2_5_37_1","doi-asserted-by":"publisher","DOI":"10.1021\/bi0478143"},{"key":"e_1_2_5_38_1","doi-asserted-by":"publisher","DOI":"10.1021\/bi047815v"},{"key":"e_1_2_5_39_1","doi-asserted-by":"publisher","DOI":"10.1002\/prot.22860"},{"key":"e_1_2_5_40_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkt1243"},{"key":"e_1_2_5_41_1","doi-asserted-by":"publisher","DOI":"10.1038\/nbt0804-1035"},{"key":"e_1_2_5_42_1","doi-asserted-by":"publisher","DOI":"10.1038\/nbt0308-274"},{"key":"e_1_2_5_43_1","doi-asserted-by":"publisher","DOI":"10.1110\/ps.04672604"},{"key":"e_1_2_5_44_1","doi-asserted-by":"publisher","DOI":"10.1107\/S0021889892009944"},{"key":"e_1_2_5_45_1","doi-asserted-by":"publisher","DOI":"10.1145\/235815.235821"}],"container-title":["Protein Science"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.wiley.com\/onlinelibrary\/tdm\/v1\/articles\/10.1002%2Fpro.3416","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/pro.3416","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1002\/pro.3416","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/api.wiley.com\/onlinelibrary\/chorus\/v1\/articles\/10.1002%2Fpro.3416","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/pro.3416","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/pro.3416","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,16]],"date-time":"2023-09-16T02:38:45Z","timestamp":1694831925000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/pro.3416"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,4,27]]},"references-count":44,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2018,6]]}},"alternative-id":["10.1002\/pro.3416"],"URL":"https:\/\/doi.org\/10.1002\/pro.3416","archive":["Portico"],"relation":{},"ISSN":["0961-8368","1469-896X"],"issn-type":[{"value":"0961-8368","type":"print"},{"value":"1469-896X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,4,27]]},"assertion":[{"value":"2017-12-21","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2018-03-26","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2018-04-27","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}