{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,12]],"date-time":"2026-04-12T09:18:27Z","timestamp":1775985507975,"version":"3.50.1"},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"11","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Many evolutionarily distant, but functionally meaningful links between proteins come to light through comparison of spatial structures. Most programs that assess structural similarity compare two proteins to each other and find regions in common between them. Structural classification experts look for a particular structural motif instead. Programs base similarity scores on superposition or closeness of either Cartesian coordinates or inter-residue contacts. Experts pay more attention to the general orientation of the main chain and mutual spatial arrangement of secondary structural elements. There is a need for a computational tool to find proteins with the same secondary structures, topological connections and spatial architecture, regardless of subtle differences in 3D coordinates.<\/jats:p><jats:p>Results: We developed ProSMoS\u2014a Protein Structure Motif Search program that emulates an expert. Starting from a spatial structure, the program uses previously delineated secondary structural elements. A meta-matrix of interactions between the elements (parallel or antiparallel) minding handedness of connections (left or right) and other features (e.g. element lengths and hydrogen bonds) is constructed prior to or during the searches. All structures are reduced to such meta-matrices that contain just enough information to define a protein fold, but this definition remains very general and deviations in 3D coordinates are tolerated. User supplies a meta-matrix for a structural motif of interest, and ProSMoS finds all proteins in the protein data bank (PDB) that match the meta-matrix. ProSMoS performance is compared to other programs and is illustrated on a \u03b2-Grasp motif. A brief analysis of all \u03b2-Grasp-containing proteins is presented.<\/jats:p><jats:p>Program availability: ProSMoS is freely available for non-commercial use from ftp:\/\/iole.swmed.edu\/pub\/ProSMoS.<\/jats:p><jats:p>Contact: \u00a0grishin@chop.swmed.edu<\/jats:p><jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm121","type":"journal-article","created":{"date-parts":[[2007,3,24]],"date-time":"2007-03-24T23:57:42Z","timestamp":1174780662000},"page":"1331-1338","source":"Crossref","is-referenced-by-count":36,"title":["Searching for three-dimensional secondary structural patterns in proteins with ProSMoS"],"prefix":"10.1093","volume":"23","author":[{"given":"Shuoyong","family":"Shi","sequence":"first","affiliation":[{"name":"2 \u00a01Howard Hughes Medical Institute and 2Department of Biochemistry, University of Texas Southwestern Medical Center, 5323, Harry Hines Blvd, Dallas, TX 75390-9050, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yi","family":"Zhong","sequence":"additional","affiliation":[{"name":"2 \u00a01Howard Hughes Medical Institute and 2Department of Biochemistry, University of Texas Southwestern Medical Center, 5323, Harry Hines Blvd, Dallas, TX 75390-9050, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Indraneel","family":"Majumdar","sequence":"additional","affiliation":[{"name":"2 \u00a01Howard Hughes Medical Institute and 2Department of Biochemistry, University of Texas Southwestern Medical Center, 5323, Harry Hines Blvd, Dallas, TX 75390-9050, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"S.","family":"Sri Krishna","sequence":"additional","affiliation":[{"name":"2 \u00a01Howard Hughes Medical Institute and 2Department of Biochemistry, University of Texas Southwestern Medical Center, 5323, Harry Hines Blvd, Dallas, TX 75390-9050, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nick V.","family":"Grishin","sequence":"additional","affiliation":[{"name":"2 \u00a01Howard Hughes Medical Institute and 2Department of Biochemistry, University of Texas Southwestern Medical Center, 5323, Harry Hines Blvd, Dallas, TX 75390-9050, USA"},{"name":"2 \u00a01Howard Hughes Medical Institute and 2Department of Biochemistry, University of Texas Southwestern Medical Center, 5323, Harry Hines Blvd, Dallas, TX 75390-9050, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2007,3,24]]},"reference":[{"key":"2023041104583863000_","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":"2023041104583863000_","doi-asserted-by":"crossref","first-page":"D226","DOI":"10.1093\/nar\/gkh039","article-title":"SCOP database in 2004: refinements integrate structure and sequence family data","volume":"32","author":"Andreeva","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023041104583863000_","doi-asserted-by":"crossref","first-page":"4205","DOI":"10.1093\/nar\/26.18.4205","article-title":"Toprim\u2013a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins","volume":"26","author":"Aravind","year":"1998","journal-title":"Nucleic Acids Res."},{"key":"2023041104583863000_","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1002\/prot.10064","article-title":"Monophyly of class I aminoacyl tRNA synthetase, USPA, ETFP, photolyase, and PP-ATPase nucleotide-binding domains: implications for protein evolution in the RNA","volume":"48","author":"Aravind","year":"2002","journal-title":"Proteins"},{"key":"2023041104583863000_","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The protein data bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"2023041104583863000_","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1002\/(SICI)1097-0134(19980201)30:2<193::AID-PROT9>3.0.CO;2-O","article-title":"Structural classification of alphabetabeta and betabetaalpha supersecondary structure units in proteins","volume":"30","author":"Boutonnet","year":"1998","journal-title":"Proteins"},{"key":"2023041104583863000_","doi-asserted-by":"crossref","first-page":"1003","DOI":"10.1016\/j.jmb.2006.06.049","article-title":"Evolutionary genomics of the HAD superfamily: understanding the structural adaptations and catalytic diversity in a superfamily of phosphoesterases and allied enzymes","volume":"361","author":"Burroughs","year":"2006","journal-title":"J. Mol. Biol."},{"key":"2023041104583863000_","doi-asserted-by":"crossref","first-page":"i81","DOI":"10.1093\/bioinformatics\/btg1009","article-title":"PSI: indexing protein structures for fast similarity search","volume":"19","author":"Camoglu","year":"2003","journal-title":"Bioinformatics"},{"key":"2023041104583863000_","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1186\/1472-6807-5-6","article-title":"A comprehensive update of the sequence and structure classification of kinases","volume":"5","author":"Cheek","year":"2005","journal-title":"BMC Struct. Biol."},{"key":"2023041104583863000_","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1016\/0097-8485(95)00075-5","article-title":"Algorithms for finding the axis of a helix: fast rotational and parametric least-squares methods","volume":"20","author":"Christopher","year":"1996","journal-title":"Comput. Chem."},{"key":"2023041104583863000_","doi-asserted-by":"crossref","first-page":"685","DOI":"10.1089\/106652701446152","article-title":"Structure comparison and structure patterns","volume":"7","author":"Eidhammer","year":"2000","journal-title":"J. Comput. Biol."},{"key":"2023041104583863000_","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1093\/protein\/gzg046","article-title":"Stranded in isolation: structural role of isolated extended strands in proteins","volume":"16","author":"Eswar","year":"2003","journal-title":"Protein Eng."},{"key":"2023041104583863000_","doi-asserted-by":"crossref","first-page":"566","DOI":"10.1002\/prot.340230412","article-title":"Knowledge-based protein secondary structure assignment","volume":"23","author":"Frishman","year":"1995","journal-title":"Proteins"},{"key":"2023041104583863000_","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1016\/S0959-440X(96)80058-3","article-title":"Surprising similarities in structure comparison","volume":"6","author":"Gibrat","year":"1996","journal-title":"Curr. Opin. Struct. Biol."},{"key":"2023041104583863000_","doi-asserted-by":"crossref","first-page":"909","DOI":"10.1016\/S0022-2836(02)00992-0","article-title":"Quantifying the similarities within fold space","volume":"323","author":"Harrison","year":"2002","journal-title":"J. Mol. Biol."},{"key":"2023041104583863000_","doi-asserted-by":"crossref","first-page":"776","DOI":"10.1038\/nrc1994","article-title":"Ubiquitin and ubiquitin-like proteins in cancer pathogenesis","volume":"6","author":"Hoeller","year":"2006","journal-title":"Nat. Rev. Cancer"},{"key":"2023041104583863000_","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1126\/science.273.5275.595","article-title":"Mapping the protein universe","volume":"273","author":"Holm","year":"1996","journal-title":"Science"},{"key":"2023041104583863000_","doi-asserted-by":"crossref","first-page":"2577","DOI":"10.1002\/bip.360221211","article-title":"Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features","volume":"22","author":"Kabsch","year":"1983","journal-title":"Biopolymers"},{"key":"2023041104583863000_","doi-asserted-by":"crossref","first-page":"340","DOI":"10.1002\/prot.10555","article-title":"CASP5 target classification","volume":"53","author":"Kinch","year":"2003","journal-title":"Proteins"},{"key":"2023041104583863000_","doi-asserted-by":"crossref","first-page":"348","DOI":"10.1016\/S0959-440X(00)00214-1","article-title":"Protein structure similarities","volume":"11","author":"Koehl","year":"2001","journal-title":"Curr. Opin. in Struct. Biol."},{"key":"2023041104583863000_","doi-asserted-by":"crossref","first-page":"946","DOI":"10.1107\/S0021889891004399","article-title":"MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures","author":"Kraulis","year":"1991","journal-title":"J. Appl. Crystallogr."},{"key":"2023041104583863000_","doi-asserted-by":"crossref","first-page":"1308","DOI":"10.1093\/bioinformatics\/bti227","article-title":"Structural drift: a possible path to protein fold change","volume":"21","author":"Krishna","year":"2005","journal-title":"Bioinformatics"},{"key":"2023041104583863000_","first-page":"2256","article-title":"Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions","volume":"60","author":"Krissinel","year":"2004","journal-title":"Acta Crystallogr"},{"key":"2023041104583863000_","doi-asserted-by":"crossref","first-page":"781","DOI":"10.1016\/j.jmb.2003.08.040","article-title":"Evolution and classification of P-loop kinases and related proteins","volume":"333","author":"Leipe","year":"2003","journal-title":"J. Mol. Biol."},{"key":"2023041104583863000_","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1016\/0263-7855(95)00037-7","article-title":"Systematic representation of protein folding patterns","volume":"13","author":"Lesk","year":"1995","journal-title":"Journal of molecular graphics"},{"key":"2023041104583863000_","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1002\/prot.340230309","article-title":"Threading a database of protein cores","volume":"23","author":"Madej","year":"1995","journal-title":"Proteins"},{"key":"2023041104583863000_","doi-asserted-by":"crossref","first-page":"202","DOI":"10.1186\/1471-2105-6-202","article-title":"PALSSE: a program to delineate linear secondary structural elements from protein structures","volume":"6","author":"Majumdar","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"2023041104583863000_","doi-asserted-by":"crossref","first-page":"D251","DOI":"10.1093\/nar\/gkh060","article-title":"TOPS: an enhanced database of protein structural topology","volume":"32","author":"Michalopoulos","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023041104583863000_","doi-asserted-by":"crossref","first-page":"452","DOI":"10.1093\/nar\/gkg062","article-title":"The CATH database: an extended protein family resource for structural and functional genomics","volume":"31","author":"Pearl","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023041104583863000_","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1002\/prot.20329","article-title":"Structural classification of thioredoxin-like fold proteins","volume":"58","author":"Qi","year":"2005","journal-title":"Proteins"},{"key":"2023041104583863000_","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1002\/prot.340030202","article-title":"Identification of structural motifs from protein coordinate data: secondary structure and first-level supersecondary structure","volume":"3","author":"Richards","year":"1988","journal-title":"Proteins"},{"key":"2023041104583863000_","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1110\/ps.03239404","article-title":"FoldMiner: structural motif discovery using an improved superposition algorithm","volume":"13","author":"Shapiro","year":"2004","journal-title":"Protein Sci."},{"key":"2023041104583863000_","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1093\/bib\/3.3.265","article-title":"PROSITE: a documented database using patterns and profiles as motif descriptors","volume":"3","author":"Sigrist","year":"2002","journal-title":"Brief. Bioinformatics"},{"key":"2023041104583863000_","doi-asserted-by":"crossref","first-page":"2537","DOI":"10.1093\/bioinformatics\/bti331","article-title":"Protein structure topological comparison, discovery and matching service","volume":"21","author":"Torrance","year":"2005","journal-title":"Bioinformatics"},{"key":"2023041104583863000_","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1016\/j.bbamcr.2004.10.005","article-title":"Ubiquitin family proteins and their relationship to the proteasome: a structural perspective","volume":"1695","author":"Walters","year":"2004","journal-title":"Biochim. Biophys. Acta."},{"key":"2023041104583863000_","first-page":"283","article-title":"Graph Algorithms","volume-title":"Data Structures and Algorithm Analysis in C.","author":"Weiss","year":"1997"},{"key":"2023041104583863000_","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1002\/1097-0134(20000815)40:3<409::AID-PROT60>3.0.CO;2-6","article-title":"A comprehensive analysis of the Greek key motifs in protein beta-barrels and beta-sandwiches","volume":"40","author":"Zhang","year":"2000","journal-title":"Proteins"},{"key":"2023041104583863000_","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1186\/1472-6807-6-12","article-title":"Secondary structure spatial conformation footprint: a novel method for fast protein structure comparison and classification","volume":"6","author":"Zotenko","year":"2006","journal-title":"BMC Struct. Biol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/11\/1331\/49813101\/bioinformatics_23_11_1331.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/11\/1331\/49813101\/bioinformatics_23_11_1331.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,12]],"date-time":"2024-02-12T10:27:30Z","timestamp":1707733650000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/23\/11\/1331\/201846"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,3,24]]},"references-count":38,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2007,6,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btm121","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2007,6]]},"published":{"date-parts":[[2007,3,24]]}}}