{"id":"https://openalex.org/W2139060596","doi":"https://doi.org/10.1093/nar/gki353","title":"Fragment Finder: a web-based software to identify similar three-dimensional structural motif","display_name":"Fragment Finder: a web-based software to identify similar three-dimensional structural motif","publication_year":2005,"publication_date":"2005-06-26","ids":{"openalex":"https://openalex.org/W2139060596","doi":"https://doi.org/10.1093/nar/gki353","mag":"2139060596","pmid":"https://pubmed.ncbi.nlm.nih.gov/15980587"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gki353","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki353","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/nar/gki353","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5029466397","display_name":"P. Ananthalakshmi","orcid":null},"institutions":[{"id":"https://openalex.org/I59270414","display_name":"Indian Institute of Science Bangalore","ror":"https://ror.org/04dese585","country_code":"IN","type":"education","lineage":["https://openalex.org/I59270414"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"P. Ananthalakshmi","raw_affiliation_strings":["Bioinformatics Centre, Indian Institute of Science, Bangalore 560 012, India"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Centre, Indian Institute of Science, Bangalore 560 012, India","institution_ids":["https://openalex.org/I59270414"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085787454","display_name":"Ch. Kiran Kumar","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ch. K. Kumar","raw_affiliation_strings":["Bioinformatics Centre and"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Centre and","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005666046","display_name":"M. Jeyasimhan","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"M. Jeyasimhan","raw_affiliation_strings":["Bioinformatics Centre and"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Centre and","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080140846","display_name":"K. Sumathi","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"K. Sumathi","raw_affiliation_strings":["Bioinformatics Centre and"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Centre and","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035649762","display_name":"K. Sekar","orcid":"https://orcid.org/0000-0002-9755-862X"},"institutions":[{"id":"https://openalex.org/I59270414","display_name":"Indian Institute of Science Bangalore","ror":"https://ror.org/04dese585","country_code":"IN","type":"education","lineage":["https://openalex.org/I59270414"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"K. Sekar","raw_affiliation_strings":["Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560 012, India","Bioinformatics Centre and"],"affiliations":[{"raw_affiliation_string":"Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560 012, India","institution_ids":["https://openalex.org/I59270414"]},{"raw_affiliation_string":"Bioinformatics Centre and","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5029466397"],"corresponding_institution_ids":["https://openalex.org/I59270414"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":0.2532,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":{"value":0.56912722,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"33","issue":"Web Server","first_page":"W85","last_page":"W88"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.995199978351593,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6897006630897522},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6572516560554504},{"id":"https://openalex.org/keywords/fragment","display_name":"Fragment (logic)","score":0.6016499996185303},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.5216648578643799},{"id":"https://openalex.org/keywords/structural-motif","display_name":"Structural motif","score":0.47161203622817993},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4568648040294647},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.44959110021591187},{"id":"https://openalex.org/keywords/search-engine","display_name":"Search engine","score":0.4393320083618164},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3341846466064453},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.32497555017471313},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3237760663032532},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.23605158925056458},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.16842159628868103},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.1397363841533661},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.08430320024490356}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6897006630897522},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6572516560554504},{"id":"https://openalex.org/C2776235265","wikidata":"https://www.wikidata.org/wiki/Q18392052","display_name":"Fragment (logic)","level":2,"score":0.6016499996185303},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.5216648578643799},{"id":"https://openalex.org/C132677234","wikidata":"https://www.wikidata.org/wiki/Q3273544","display_name":"Structural motif","level":2,"score":0.47161203622817993},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4568648040294647},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.44959110021591187},{"id":"https://openalex.org/C97854310","wikidata":"https://www.wikidata.org/wiki/Q19541","display_name":"Search engine","level":2,"score":0.4393320083618164},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3341846466064453},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.32497555017471313},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3237760663032532},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.23605158925056458},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.16842159628868103},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1397363841533661},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.08430320024490356}],"mesh":[{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1093/nar/gki353","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki353","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:15980587","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15980587","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:eprints.iisc.ac.in:3403","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4377196309","display_name":"NOT FOUND REPOSITORY (Indian Institute of Science Bangalore)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I59270414","host_organization_name":"Indian Institute of Science Bangalore","host_organization_lineage":["https://openalex.org/I59270414"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.582.5516","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.582.5516","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://eprints.iisc.ernet.in/3403/1/Fragment_Finder.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.95.8347","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.95.8347","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://nar.oxfordjournals.org/cgi/screenpdf/33/suppl_2/W85.pdf","raw_type":"text"},{"id":"pmh:oai:europepmc.org:155152","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1160114","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gki353","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki353","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320290","display_name":"University of Oxford","ror":"https://ror.org/052gg0110"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":10,"referenced_works":["https://openalex.org/W1521782084","https://openalex.org/W1966041739","https://openalex.org/W1967149946","https://openalex.org/W1968815144","https://openalex.org/W2005631746","https://openalex.org/W2026258231","https://openalex.org/W2084367350","https://openalex.org/W2102306820","https://openalex.org/W2130479394","https://openalex.org/W2168211076"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2998485758","https://openalex.org/W2323581027","https://openalex.org/W2892146921","https://openalex.org/W2044846275","https://openalex.org/W1742055567","https://openalex.org/W2089595571","https://openalex.org/W1594009522","https://openalex.org/W3208481717","https://openalex.org/W2522990033"],"abstract_inverted_index":{"FF":[0],"(Fragment":[1],"Finder)":[2],"is":[3,31,94],"a":[4],"web-based":[5],"interactive":[6],"search":[7,30],"engine":[8,74],"developed":[9],"to":[10,53,77],"retrieve":[11],"the":[12,19,34,37,47,58,64,79,87,99],"user-desired":[13],"similar":[14,57],"3D":[15,84],"structural":[16,59],"fragments":[17,60],"from":[18],"selected":[20],"subset":[21],"of":[22,36],"25":[23],"or":[24,82,103],"90%":[25],"non-homologous":[26],"protein":[27],"chains.":[28],"The":[29,73,90],"based":[32],"on":[33,86],"comparison":[35],"main":[38],"chain":[39],"backbone":[40],"conformational":[41],"angles":[42],"(phi":[43],"and":[44],").":[45],"Additionally,":[46],"queried":[48],"motifs":[49],"can":[50,66],"be":[51,67],"superimposed":[52],"find":[54],"out":[55],"how":[56],"are,":[61],"so":[62],"that":[63],"information":[65],"effectively":[68],"used":[69],"in":[70],"molecular":[71],"modeling.":[72],"has":[75],"facilities":[76],"view":[78],"resultant":[80],"superposed":[81],"individual":[83],"structure(s)":[85],"client":[88],"machine.":[89],"proposed":[91],"web":[92],"server":[93],"made":[95],"freely":[96],"accessible":[97],"at":[98],"following":[100],"URL:":[101],"http://cluster.physics.iisc.ernet.in/ff/":[102],"http://144.16.71.148/ff/.":[104]},"counts_by_year":[{"year":2023,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2014,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
