{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,14]],"date-time":"2026-07-14T01:52:47Z","timestamp":1783993967011,"version":"3.55.0"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"6","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Currently, 25% of proteins annotated in Pfam have their function unknown. One way of predicting proteins function is by looking at their active site, which has two main parts: the catalytic site and the substrate binding site. The active site is more conserved than the other residues of the protein and can be a rich source of information for protein function prediction. This article presents a new heuristic method, named genetic active site search (GASS), which searches for given active site 3D templates in unknown proteins. The method can perform non-exact amino acid matches (conservative mutations), is able to find amino acids in different chains and does not impose any restrictions on the active site size.<\/jats:p>\n               <jats:p>Results: GASS results were compared with those catalogued in the catalytic site atlas (CSA) in four different datasets and compared with two other methods: amino acid pattern search for substructures and motif and catalytic site identification. The results show GASS can correctly identify &amp;gt;90% of the templates searched. Experiments were also run using data from the substrate binding sites prediction competition CASP 10, and GASS is ranked fourth among the 18 methods considered.<\/jats:p>\n               <jats:p>Availability and implementation: Source code and datasets (dcc.ufmg.br\/ \u223cglpappa\/gass).<\/jats:p>\n               <jats:p>Contact: \u00a0sandroizidoro@unifei.edu.br<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu746","type":"journal-article","created":{"date-parts":[[2014,11,12]],"date-time":"2014-11-12T04:44:24Z","timestamp":1415767464000},"page":"864-870","source":"Crossref","is-referenced-by-count":27,"title":["GASS: identifying enzyme active sites with genetic algorithms"],"prefix":"10.1093","volume":"31","author":[{"given":"Sandro C.","family":"Izidoro","sequence":"first","affiliation":[{"name":"1 Advanced Campus at Itabira, Universidade Federal de Itajub\u00e1, Itajub\u00e1, MG 35903-087, Brazil and 2Department of Computer Science and 3Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Raquel C.","family":"de Melo-Minardi","sequence":"additional","affiliation":[{"name":"1 Advanced Campus at Itabira, Universidade Federal de Itajub\u00e1, Itajub\u00e1, MG 35903-087, Brazil and 2Department of Computer Science and 3Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil"},{"name":"1 Advanced Campus at Itabira, Universidade Federal de Itajub\u00e1, Itajub\u00e1, MG 35903-087, Brazil and 2Department of Computer Science and 3Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gisele L.","family":"Pappa","sequence":"additional","affiliation":[{"name":"1 Advanced Campus at Itabira, Universidade Federal de Itajub\u00e1, Itajub\u00e1, MG 35903-087, Brazil and 2Department of Computer Science and 3Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil"},{"name":"1 Advanced Campus at Itabira, Universidade Federal de Itajub\u00e1, Itajub\u00e1, MG 35903-087, Brazil and 2Department of Computer Science and 3Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2014,11,10]]},"reference":[{"key":"2023020116175566700_btu746-B1","doi-asserted-by":"crossref","first-page":"1408","DOI":"10.1002\/prot.22655","article-title":"Mapping of ligand-binding cavities in proteins","volume":"78","author":"Andersson","year":"2010","journal-title":"Proteins"},{"key":"2023020116175566700_btu746-B2","doi-asserted-by":"crossref","DOI":"10.1887\/0750308958","volume-title":"Handbook of Evolutionary Computation","author":"Back","year":"1997"},{"key":"2023020116175566700_btu746-B3","doi-asserted-by":"crossref","first-page":"1644","DOI":"10.1093\/bioinformatics\/btg226","article-title":"An algorithm for constraint-based structural template matching: application to 3d templates with statistical analysis","volume":"19","author":"Barker","year":"2003","journal-title":"Bioinformatics"},{"key":"2023020116175566700_btu746-B4","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1016\/S0022-2836(02)01036-7","article-title":"Analysis of catalytic residues in enzyme active sites","volume":"324","author":"Bartlett","year":"2002","journal-title":"J. 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