{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,7,6]],"date-time":"2024-07-06T13:22:51Z","timestamp":1720272171450},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"7","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Structural genomics initiatives are increasingly leading to the determination of the 3D structure of target proteins whose catalytic function is not known. The aim of this work was that of developing a novel versatile tool for searching structural similarity, which allows to predict the catalytic function, if any, of these proteins.<\/jats:p>\n               <jats:p>Results: The algorithm implemented by the tool is based on local structural comparison to find the largest subset of similar residues between an input protein and known functional sites. The method uses a geometric hashing approach where information related to residue pairs from the input structures is stored in a hash table and then is quickly retrieved during the comparison step. Tests on proteins belonging to different functional classes, done using the Catalytic Site Atlas entries as targets, indicate that the algorithm is able to identify the correct functional class of the input protein in the vast majority of the cases.<\/jats:p>\n               <jats:p>Availability and implementation: The application was developed in Java SE 6, with a Java Swing Graphic User Interface (GUI). The system can be run locally on any operating system (OS) equipped with a suitable Java Virtual Machine, and is available at the following URL: http:\/\/www.computationalbiology.it\/software\/ASSISTv1.zip.<\/jats:p>\n               <jats:p>Contact: \u00a0polticel@uniroma3.it<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt664","type":"journal-article","created":{"date-parts":[[2013,11,16]],"date-time":"2013-11-16T04:52:14Z","timestamp":1384577534000},"page":"1022-1024","source":"Crossref","is-referenced-by-count":14,"title":["ASSIST: a fast versatile local structural comparison tool"],"prefix":"10.1093","volume":"30","author":[{"given":"Silvia","family":"Caprari","sequence":"first","affiliation":[{"name":"1 Department of Sciences, University of Roma Tre, 00146 Rome, 2Department of Information and Electric Engineering and Applied Mathematics, University of Salerno, 84084 Fisciano, Italy, 3Artificial Solutions, 08026 Barcelona, Spain and 4National Institute of Nuclear Physics, Roma Tre Section, 00146 Rome, Italy"}]},{"given":"Daniele","family":"Toti","sequence":"additional","affiliation":[{"name":"1 Department of Sciences, University of Roma Tre, 00146 Rome, 2Department of Information and Electric Engineering and Applied Mathematics, University of Salerno, 84084 Fisciano, Italy, 3Artificial Solutions, 08026 Barcelona, Spain and 4National Institute of Nuclear Physics, Roma Tre Section, 00146 Rome, Italy"}]},{"given":"Le","family":"Viet Hung","sequence":"additional","affiliation":[{"name":"1 Department of Sciences, University of Roma Tre, 00146 Rome, 2Department of Information and Electric Engineering and Applied Mathematics, University of Salerno, 84084 Fisciano, Italy, 3Artificial Solutions, 08026 Barcelona, Spain and 4National Institute of Nuclear Physics, Roma Tre Section, 00146 Rome, Italy"}]},{"given":"Maurizio","family":"Di Stefano","sequence":"additional","affiliation":[{"name":"1 Department of Sciences, University of Roma Tre, 00146 Rome, 2Department of Information and Electric Engineering and Applied Mathematics, University of Salerno, 84084 Fisciano, Italy, 3Artificial Solutions, 08026 Barcelona, Spain and 4National Institute of Nuclear Physics, Roma Tre Section, 00146 Rome, Italy"}]},{"given":"Fabio","family":"Polticelli","sequence":"additional","affiliation":[{"name":"1 Department of Sciences, University of Roma Tre, 00146 Rome, 2Department of Information and Electric Engineering and Applied Mathematics, University of Salerno, 84084 Fisciano, Italy, 3Artificial Solutions, 08026 Barcelona, Spain and 4National Institute of Nuclear Physics, Roma Tre Section, 00146 Rome, Italy"},{"name":"1 Department of Sciences, University of Roma Tre, 00146 Rome, 2Department of Information and Electric Engineering and Applied Mathematics, University of Salerno, 84084 Fisciano, Italy, 3Artificial Solutions, 08026 Barcelona, Spain and 4National Institute of Nuclear Physics, Roma Tre Section, 00146 Rome, Italy"}]}],"member":"286","published-online":{"date-parts":[[2013,11,15]]},"reference":[{"key":"2023012710445585600_btt664-B1","first-page":"3590","article-title":"PRINTS-a database of protein motif fingerprints","volume":"22","author":"Attwood","year":"1994","journal-title":"Nucleic Acids Res."},{"key":"2023012710445585600_btt664-B2","first-page":"3583","article-title":"PROSITE: recent developments","volume":"22","author":"Bairoch","year":"1994","journal-title":"Nucleic Acids Res."},{"key":"2023012710445585600_btt664-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":"2023012710445585600_btt664-B4","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1038\/13783","article-title":"Structural genomics: beyond the human genome project","volume":"23","author":"Burley","year":"1999","journal-title":"Nat. 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