{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,12]],"date-time":"2026-05-12T13:56:32Z","timestamp":1778594192921,"version":"3.51.4"},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"6","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: The rapidly growing protein structure repositories have opened up new opportunities for discovery and analysis of functional and evolutionary relationships among proteins. Detecting conserved structural sites that are unique to a protein family is of great value in identification of functionally important atoms and residues. Currently available methods are computationally expensive and fail to detect biologically significant local features.<\/jats:p><jats:p>Results: We propose Local Feature Mining in Proteins (LFM-Pro) as a framework for automatically discovering family-specific local sites and the features associated with these sites. Our method uses the distance field to backbone atoms to detect geometrically significant structural centers of the protein. A feature vector is generated from the geometrical and biochemical environment around these centers. These features are then scored using a statistical measure, for their ability to distinguish a family of proteins from a background set of unrelated proteins, and successful features are combined into a representative set for the protein family. The utility and success of LFM-Pro are demonstrated on trypsin-like serine proteases family of proteins and on a challenging classification dataset via comparison with DALI. The results verify that our method is successful both in identifying the distinctive sites of a given family of proteins, and in classifying proteins using the extracted features.<\/jats:p><jats:p>Availability: The software and the datasets are freely available for academic research use at http:\/\/bioinfo.ceng.metu.edu.tr\/Pub\/LFMPro<\/jats:p><jats:p>Contact: \u00a0ahmet@ceng.metu.edu.tr, ozturk@cse.ohiostate.edu,hakan@cse.ohiostate.edu,yusu@cse.ohiostate.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl685","type":"journal-article","created":{"date-parts":[[2007,1,20]],"date-time":"2007-01-20T01:12:50Z","timestamp":1169255570000},"page":"709-716","source":"Crossref","is-referenced-by-count":20,"title":["LFM-Pro: a tool for detecting significant local structural sites in proteins"],"prefix":"10.1093","volume":"23","author":[{"given":"Ahmet","family":"Sacan","sequence":"first","affiliation":[{"name":"1 Department of Computer Engineering, Middle East Technical University, Ankara, Turkey, 2Computer Science and Engineering Department and 3Biomedical Informatics Department, The Ohio State University, Columbus, OH, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ozgur","family":"Ozturk","sequence":"additional","affiliation":[{"name":"1 Department of Computer Engineering, Middle East Technical University, Ankara, Turkey, 2Computer Science and Engineering Department and 3Biomedical Informatics Department, The Ohio State University, Columbus, OH, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hakan","family":"Ferhatosmanoglu","sequence":"additional","affiliation":[{"name":"1 Department of Computer Engineering, Middle East Technical University, Ankara, Turkey, 2Computer Science and Engineering Department and 3Biomedical Informatics Department, The Ohio State University, Columbus, OH, USA"},{"name":"1 Department of Computer Engineering, Middle East Technical University, Ankara, Turkey, 2Computer Science and Engineering Department and 3Biomedical Informatics Department, The Ohio State University, Columbus, OH, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yusu","family":"Wang","sequence":"additional","affiliation":[{"name":"1 Department of Computer Engineering, Middle East Technical University, Ankara, Turkey, 2Computer Science and Engineering Department and 3Biomedical Informatics Department, The Ohio State University, Columbus, OH, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2007,1,19]]},"reference":[{"key":"2023041107502605000_","first-page":"622","article-title":"Characterizing the microenvironment surrounding protein sites.","volume-title":"Protein Sci","author":"Bagley","year":"1995"},{"key":"2023041107502605000_","first-page":"254","article-title":"The astral compendium for sequence and structure analysis.","volume-title":"Nucleic Acids Res.","author":"Brenner","year":"2000"},{"key":"2023041107502605000_","article-title":"The cgal project-release 3.1","author":"CGAL","year":"2006"},{"key":"2023041107502605000_","first-page":"511","article-title":"Topological persistence and simplification.","volume-title":"Discrete Comput. Geom","author":"Edelsbrunner","year":"2002"},{"key":"2023041107502605000_","first-page":"3557","article-title":"Decomposition of the linking number of a closed ribbon: a problem from molecular biology.","volume-title":"Proc. Natl Acad. Sci. USA","author":"Fuller","year":"1978"},{"key":"2023041107502605000_","first-page":"285","article-title":"The flow complex: a data structure for geometric modeling. In","volume-title":"Proceedings of the 14th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA)","author":"Giesen","year":"2003"},{"key":"2023041107502605000_","doi-asserted-by":"crossref","first-page":"849","DOI":"10.1021\/jm00145a002","article-title":"A computational procedure for determining energetically favorable binding sites on biologically important macromolecules.","volume":"28","author":"Goodford","year":"1985","journal-title":"J. Med. Chem."},{"key":"2023041107502605000_","first-page":"1","article-title":"The elucidation of protein function by sequence motif analysis.","volume-title":"Computer Appl. Biosci. (CABIOS)","author":"Hodgman","year":"1989"},{"key":"2023041107502605000_","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1006\/jmbi.1993.1489","article-title":"Protein structure comparison by alignment of distance matrices.","volume":"233","author":"Holm","year":"1993","journal-title":"J. Mol. Biol"},{"key":"2023041107502605000_","doi-asserted-by":"crossref","first-page":"657","DOI":"10.1089\/cmb.2005.12.657","article-title":"Comparing graph representations of protein structure for mining family specific residue-based packing motifs.","volume":"12","author":"Huan","year":"2005","journal-title":"J. Computa. Biol"},{"key":"2023041107502605000_","first-page":"308","article-title":"Mining family specific residue packing patterns from protein structure graphs.","volume-title":"Proc. of 8th Ann. Intl. Conf. on Research in Comp. Molecular Bio. (RECOMB)","author":"Huan","year":"2004"},{"key":"2023041107502605000_","doi-asserted-by":"crossref","first-page":"362","DOI":"10.1093\/bioinformatics\/18.2.362","article-title":"Structure motif discovery and mining the PDB.","volume":"18","author":"Jonassen","year":"2001","journal-title":"Bioinformatics"},{"key":"2023041107502605000_","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1002\/1097-0282(20001015)54:5<307::AID-BIP20>3.0.CO;2-Y","article-title":"Computation of writhe in modeling of supercoiled DNA.","volume":"54","author":"Klenin","year":"2000","journal-title":"Biopolymers"},{"key":"2023041107502605000_","doi-asserted-by":"crossref","first-page":"723","DOI":"10.1016\/S0022-2836(83)80129-6","article-title":"Protein folding by restrained energy minimization and molecular dynamics.","volume":"170","author":"Levitt","year":"1983","journal-title":"J. Mol. Biol"},{"key":"2023041107502605000_","article-title":"Automatically deriving multi-level protein structures through data mining.","volume-title":"HiPC Workshop on Bioinformatics and Computational Biology","author":"Li","year":"2001"},{"key":"2023041107502605000_","doi-asserted-by":"crossref","first-page":"3324","DOI":"10.1093\/nar\/gkg553","article-title":"Webfeature: an interactive web tool for identifying and visualizing functional sites on macromolecular structures.","volume":"31","author":"Liang","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"2023041107502605000_","first-page":"543","article-title":"Common structural cliques: a tool for protein structure and function analysis.","volume-title":"Protein Eng.","author":"Milik","year":"2003"},{"key":"2023041107502605000_","first-page":"1467","article-title":"Statistical significance of hierarchical multi-body potentials based on delaunay tessellation and their application in sequence-structure alignment.","volume-title":"Protein Sci","author":"Munson","year":"1997"},{"key":"2023041107502605000_","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1016\/S0022-2836(05)80134-2","article-title":"SCOP: a structural classification of proteins database for the investigation of sequences and structures.","volume":"247","author":"Murzin","year":"1995","journal-title":"J. Mol. Biol"},{"key":"2023041107502605000_","first-page":"119","article-title":"Automatic classification of protein structure by using Gauss integrals.","volume-title":"Proc. Natl. Acad. Sci. USA","author":"Rogen","year":"2003"},{"key":"2023041107502605000_","doi-asserted-by":"crossref","first-page":"440","DOI":"10.1007\/11415770_33","article-title":"Recognition of binding patterns common to a set of protein structure.","volume":"3500","author":"Shatsky","year":"2005","journal-title":"Lecture Notes Computer Sci."},{"key":"2023041107502605000_","first-page":"228","article-title":"Identifying structural motifs in proteins.","volume-title":"Pac. Symp. Biocomput","author":"Singh","year":"2003"},{"key":"2023041107502605000_","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1089\/cmb.1996.3.213","article-title":"Delaunay tessellation of proteins.","volume":"3","author":"Singh","year":"1996","journal-title":"J. Comput. Biol."},{"key":"2023041107502605000_","doi-asserted-by":"crossref","first-page":"412","DOI":"10.1021\/ci0255984","article-title":"Searching for patterns of amino acids in 3D protein structures.","volume":"43","author":"Spriggs","year":"2003","journal-title":"J. Chem. Inf. Comput. Sci"},{"key":"2023041107502605000_","doi-asserted-by":"crossref","first-page":"2515","DOI":"10.1016\/S0006-3495(98)77960-3","article-title":"The elastic rod model for DNA and its application to the tertiary structure of dna minicircles in mononucleosomes.","volume":"74","author":"Swigon","year":"1998","journal-title":"Biophys. J."},{"key":"2023041107502605000_","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1016\/0959-440X(91)90030-W","article-title":"Templates, consensus patterns and motifs.","volume":"1","author":"Taylor","year":"1991","journal-title":"Cur. Opin. Struct. 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