{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T08:30:11Z","timestamp":1790843411692,"version":"4.1.0"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"15","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Summary: Transporters are proteins that are involved in the movement of ions or molecules across biological membranes. Currently, our knowledge about the functions of transporters is limited due to the paucity of their 3D structures. Hence, computational techniques are necessary to annotate the functions of transporters. In this work, we focused on an important functional aspect of transporters, namely annotation of targets for transport proteins. We have systematically analyzed four major classes of transporters with different transporter targets: (i) electron, (ii) protein\/mRNA, (iii) ion and (iv) others, using amino acid properties. We have developed a radial basis function network-based method for predicting transport targets with amino acid properties and position specific scoring matrix profiles. Our method showed a 10-fold cross-validation accuracy of 90.1, 80.1, 70.3 and 82.3% for electron transporters, protein\/mRNA transporters, ion transporters and others, respectively, in a dataset of 543 transporters. We have also evaluated the performance of the method with an independent dataset of 108 proteins and we obtained similar accuracy. We suggest that our method could be an effective tool for functional annotation of transport proteins.<\/jats:p><jats:p>Availability: \u00a0http:\/\/rbf.bioinfo.tw\/~sachen\/ttrbf.html<\/jats:p><jats:p>Contact: \u00a0yien@csie.org; gromiha@iitm.ac.in<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr340","type":"journal-article","created":{"date-parts":[[2011,6,9]],"date-time":"2011-06-09T00:23:48Z","timestamp":1307579028000},"page":"2062-2067","source":"Crossref","is-referenced-by-count":86,"title":["Prediction of transporter targets using efficient RBF networks with PSSM profiles and biochemical properties"],"prefix":"10.1093","volume":"27","author":[{"given":"Shu-An","family":"Chen","sequence":"first","affiliation":[{"name":"1 Department of Computer Science and Engineering, Yuan Ze University, Chung-Li, Taiwan, 2Department of Biotechnology, Indian Institute of Technology (IIT) Madras, Chennai 600 036, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu-Yen","family":"Ou","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science and Engineering, Yuan Ze University, Chung-Li, Taiwan, 2Department of Biotechnology, Indian Institute of Technology (IIT) Madras, Chennai 600 036, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tzong-Yi","family":"Lee","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science and Engineering, Yuan Ze University, Chung-Li, Taiwan, 2Department of Biotechnology, Indian Institute of Technology (IIT) Madras, Chennai 600 036, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M. Michael","family":"Gromiha","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science and Engineering, Yuan Ze University, Chung-Li, Taiwan, 2Department of Biotechnology, Indian Institute of Technology (IIT) Madras, Chennai 600 036, India"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2011,6,8]]},"reference":[{"key":"2023012511532490200_B1","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1093\/bioinformatics\/btg432","article-title":"Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information","volume":"20","author":"Ahmad","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012511532490200_B2","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":"2023012511532490200_B3","doi-asserted-by":"crossref","first-page":"498","DOI":"10.1371\/journal.pcbi.0030052","article-title":"Positive and negative design in stability and thermal adaptation of natural proteins","volume":"3","author":"Berezovsky","year":"2007","journal-title":"PLoS Comput. 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Biol. Chem."},{"key":"2023012511532490200_B10","doi-asserted-by":"crossref","first-page":"D201","DOI":"10.1093\/nar\/gkn672","article-title":"TMFunction: database for functional residues in membrane proteins","volume":"37","author":"Gromiha","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023012511532490200_B11","doi-asserted-by":"crossref","first-page":"378","DOI":"10.1093\/bioinformatics\/14.4.378","article-title":"SOSUI: classification and secondary structure prediction system for membrane proteins","volume":"14","author":"Hirokawa","year":"1998","journal-title":"Bioinformatics"},{"key":"2023012511532490200_B12","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1016\/S1016-8478(23)13783-6","article-title":"Discovering the interaction propensities of amino acids and nucleotides from protein-RNA complexes","volume":"16","author":"Jeong","year":"2003","journal-title":"Mol. 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