{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,18]],"date-time":"2025-12-18T13:50:52Z","timestamp":1766065852466},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"6","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Detecting homologous proteins is one of the fundamental problems in computational biology. Many tools to solve this problem have been developed, but development of a simple, effective and generally applicable method is still desirable.<\/jats:p>\n               <jats:p>Results: We propose a simple but effective information retrieval approach, named SIMPRO, to identify homology relationship between proteins. The key idea of our approach is that by accumulating and comparing indirect signals from conventional homology search methods, the search sensitivity can be increased. We tested the idea on the problem of detecting homology relationship between Pfam families, as well as detecting structural homologs based on SCOP, and found that our method achieved significant improvement. Our results indicate that simple manipulation of conventional homology search outputs by SIMPRO algorithm can remarkably improve homology search accuracy.<\/jats:p>\n               <jats:p>Contact: \u00a0kds@kaist.ac.kr<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp048","type":"journal-article","created":{"date-parts":[[2009,1,23]],"date-time":"2009-01-23T01:13:55Z","timestamp":1232673235000},"page":"729-735","source":"Crossref","is-referenced-by-count":8,"title":["SIMPRO: simple protein homology detection method by using indirect signals"],"prefix":"10.1093","volume":"25","author":[{"given":"Inkyung","family":"Jung","sequence":"first","affiliation":[{"name":"1 Department of Bio and Brain Engineering and 2KAIST Institute for BioCentury, KAIST, Daejeon 305-701, South Korea"}]},{"given":"Dongsup","family":"Kim","sequence":"additional","affiliation":[{"name":"1 Department of Bio and Brain Engineering and 2KAIST Institute for BioCentury, KAIST, Daejeon 305-701, South Korea"},{"name":"1 Department of Bio and Brain Engineering and 2KAIST Institute for BioCentury, KAIST, Daejeon 305-701, South Korea"}]}],"member":"286","published-online":{"date-parts":[[2009,1,22]]},"reference":[{"key":"2023051209125385200_B1","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"2023051209125385200_B2","doi-asserted-by":"crossref","first-page":"809","DOI":"10.1093\/bioinformatics\/btm034","article-title":"SCOOP: a simple method for identification of novel protein superfamily relationships","volume":"23","author":"Bateman","year":"2007","journal-title":"Bioinformatics"},{"key":"2023051209125385200_B3","doi-asserted-by":"crossref","first-page":"D189","DOI":"10.1093\/nar\/gkh034","article-title":"The ASTRAL Compendium in 2004","volume":"32","author":"Chandonia","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023051209125385200_B4","doi-asserted-by":"crossref","first-page":"1301","DOI":"10.1093\/bioinformatics\/bth090","article-title":"A comparison of scoring functions for protein sequence profile alignment","volume":"20","author":"Edgar","year":"2004","journal-title":"Bioinformatics"},{"key":"2023051209125385200_B5","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1016\/S0097-8485(96)80004-0","article-title":"The use of receiver operating characteristic (ROC) analysis to evaluate sequence matching","volume":"20","author":"Gribskov","year":"1996","journal-title":"Computers Chem."},{"key":"2023051209125385200_B6","doi-asserted-by":"crossref","first-page":"2667","DOI":"10.1093\/bioinformatics\/bti384","article-title":"Fold recognition by combining profile-profile alignment and support vector machine","volume":"21","author":"Han","year":"2005","journal-title":"Bioinformatics"},{"key":"2023051209125385200_B7","doi-asserted-by":"crossref","first-page":"298","DOI":"10.1186\/1471-2105-9-298","article-title":"Application of nonnegative matrix factorization to improve profile-profile alignment features for fold recognition and remote homolog detection","volume":"9","author":"Jung","year":"2008","journal-title":"BMC Bioinformatics"},{"issue":"Suppl. 3","key":"2023051209125385200_B8","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1002\/(SICI)1097-0134(1999)37:3+<121::AID-PROT16>3.0.CO;2-Q","article-title":"Predicting protein structure using only sequence information","author":"Karplus","year":"1999","journal-title":"Proteins"},{"key":"2023051209125385200_B9","doi-asserted-by":"crossref","first-page":"641","DOI":"10.1093\/protein\/gzg081","article-title":"PROSPECT II: protein structure prediction program for genome-scale applications","volume":"16","author":"Kim","year":"2003","journal-title":"Protein Eng."},{"key":"2023051209125385200_B10","doi-asserted-by":"crossref","first-page":"282","DOI":"10.1186\/1471-2105-6-282","article-title":"The distance-profile representation and its application to detection of distantly related protein families","volume":"6","author":"Ku","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"2023051209125385200_B11","doi-asserted-by":"crossref","first-page":"1339","DOI":"10.1093\/bioinformatics\/btn130","article-title":"Simple is beautiful: a straightforward approach to improve the delineation of true and false positives in PSI-BLAST searches","volume":"24","author":"Lee","year":"2008","journal-title":"Bioinformatics"},{"key":"2023051209125385200_B12","doi-asserted-by":"crossref","first-page":"857","DOI":"10.1089\/106652703322756113","article-title":"Combining pairwise sequence similarity and support vector machines for detecting remote protein evolutionary and structural relationships","volume":"10","author":"Liao","year":"2003","journal-title":"J. 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