{"id":"https://openalex.org/W2018575421","doi":"https://doi.org/10.1021/ci9801623","title":"Clustering Peptide Structures through Identification of Commonly Exposed Groups","display_name":"Clustering Peptide Structures through Identification of Commonly Exposed Groups","publication_year":1999,"publication_date":"1999-04-17","ids":{"openalex":"https://openalex.org/W2018575421","doi":"https://doi.org/10.1021/ci9801623","mag":"2018575421"},"language":"en","primary_location":{"id":"doi:10.1021/ci9801623","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci9801623","pdf_url":null,"source":{"id":"https://openalex.org/S171559003","display_name":"Journal of Chemical Information and Computer Sciences","issn_l":"0095-2338","issn":["0095-2338","1520-5142"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Computer Sciences","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5002965116","display_name":"Thy-Hou Lin","orcid":null},"institutions":[{"id":"https://openalex.org/I148366613","display_name":"National Yang Ming Chiao Tung University","ror":"https://ror.org/00se2k293","country_code":"TW","type":"education","lineage":["https://openalex.org/I148366613"]},{"id":"https://openalex.org/I25846049","display_name":"National Tsing Hua University","ror":"https://ror.org/00zdnkx70","country_code":"TW","type":"education","lineage":["https://openalex.org/I25846049"]}],"countries":["TW"],"is_corresponding":true,"raw_author_name":"Thy-Hou Lin","raw_affiliation_strings":["Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan, ROC, and Department of Internal Medicine, Veterans General Hospital and National Yang-Ming University, Taipei, Taiwan, ROC"],"affiliations":[{"raw_affiliation_string":"Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan, ROC, and Department of Internal Medicine, Veterans General Hospital and National Yang-Ming University, Taipei, Taiwan, ROC","institution_ids":["https://openalex.org/I25846049","https://openalex.org/I148366613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070701593","display_name":"Jia-Jiunn Lin","orcid":null},"institutions":[{"id":"https://openalex.org/I25846049","display_name":"National Tsing Hua University","ror":"https://ror.org/00zdnkx70","country_code":"TW","type":"education","lineage":["https://openalex.org/I25846049"]},{"id":"https://openalex.org/I148366613","display_name":"National Yang Ming Chiao Tung University","ror":"https://ror.org/00se2k293","country_code":"TW","type":"education","lineage":["https://openalex.org/I148366613"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Jia-Jiunn Lin","raw_affiliation_strings":["Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan, ROC, and Department of Internal Medicine, Veterans General Hospital and National Yang-Ming University, Taipei, Taiwan, ROC"],"affiliations":[{"raw_affiliation_string":"Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan, ROC, and Department of Internal Medicine, Veterans General Hospital and National Yang-Ming University, Taipei, Taiwan, ROC","institution_ids":["https://openalex.org/I25846049","https://openalex.org/I148366613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109106417","display_name":"Yung-Feng Huang","orcid":null},"institutions":[{"id":"https://openalex.org/I148366613","display_name":"National Yang Ming Chiao Tung University","ror":"https://ror.org/00se2k293","country_code":"TW","type":"education","lineage":["https://openalex.org/I148366613"]},{"id":"https://openalex.org/I25846049","display_name":"National Tsing Hua University","ror":"https://ror.org/00zdnkx70","country_code":"TW","type":"education","lineage":["https://openalex.org/I25846049"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Yung-Feng Huang","raw_affiliation_strings":["Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan, ROC, and Department of Internal Medicine, Veterans General Hospital and National Yang-Ming University, Taipei, Taiwan, ROC"],"affiliations":[{"raw_affiliation_string":"Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan, ROC, and Department of Internal Medicine, Veterans General Hospital and National Yang-Ming University, Taipei, Taiwan, ROC","institution_ids":["https://openalex.org/I25846049","https://openalex.org/I148366613"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100659980","display_name":"Liu H","orcid":"https://orcid.org/0000-0001-8201-5529"},"institutions":[{"id":"https://openalex.org/I25846049","display_name":"National Tsing Hua University","ror":"https://ror.org/00zdnkx70","country_code":"TW","type":"education","lineage":["https://openalex.org/I25846049"]},{"id":"https://openalex.org/I148366613","display_name":"National Yang Ming Chiao Tung University","ror":"https://ror.org/00se2k293","country_code":"TW","type":"education","lineage":["https://openalex.org/I148366613"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Jin-Hwang Liu","raw_affiliation_strings":["Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan, ROC, and Department of Internal Medicine, Veterans General Hospital and National Yang-Ming University, Taipei, Taiwan, ROC"],"affiliations":[{"raw_affiliation_string":"Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan, ROC, and Department of Internal Medicine, Veterans General Hospital and National Yang-Ming University, Taipei, Taiwan, ROC","institution_ids":["https://openalex.org/I25846049","https://openalex.org/I148366613"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5002965116"],"corresponding_institution_ids":["https://openalex.org/I148366613","https://openalex.org/I25846049"],"apc_list":null,"apc_paid":null,"fwci":0.23,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.49224765,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"39","issue":"3","first_page":"622","last_page":"629"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9994999766349792,"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":0.9994999766349792,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9973000288009644,"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.996999979019165,"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/cluster-analysis","display_name":"Cluster analysis","score":0.8572795391082764},{"id":"https://openalex.org/keywords/hierarchical-clustering","display_name":"Hierarchical clustering","score":0.6825791001319885},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.5732545256614685},{"id":"https://openalex.org/keywords/group","display_name":"Group (periodic table)","score":0.5006628036499023},{"id":"https://openalex.org/keywords/block","display_name":"Block (permutation group theory)","score":0.4952799379825592},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.48871898651123047},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4842626750469208},{"id":"https://openalex.org/keywords/complete-linkage-clustering","display_name":"Complete-linkage clustering","score":0.4479755461215973},{"id":"https://openalex.org/keywords/single-linkage-clustering","display_name":"Single-linkage clustering","score":0.440290629863739},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4138016700744629},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3849780857563019},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.3541101813316345},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3258393406867981},{"id":"https://openalex.org/keywords/correlation-clustering","display_name":"Correlation clustering","score":0.298591673374176},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2177358865737915},{"id":"https://openalex.org/keywords/cure-data-clustering-algorithm","display_name":"CURE data clustering algorithm","score":0.19292110204696655},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.18213453888893127},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.17750659584999084},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.06767198443412781}],"concepts":[{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.8572795391082764},{"id":"https://openalex.org/C92835128","wikidata":"https://www.wikidata.org/wiki/Q1277447","display_name":"Hierarchical clustering","level":3,"score":0.6825791001319885},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.5732545256614685},{"id":"https://openalex.org/C2781311116","wikidata":"https://www.wikidata.org/wiki/Q83306","display_name":"Group (periodic table)","level":2,"score":0.5006628036499023},{"id":"https://openalex.org/C2777210771","wikidata":"https://www.wikidata.org/wiki/Q4927124","display_name":"Block (permutation group theory)","level":2,"score":0.4952799379825592},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.48871898651123047},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4842626750469208},{"id":"https://openalex.org/C23822008","wikidata":"https://www.wikidata.org/wiki/Q5156437","display_name":"Complete-linkage clustering","level":5,"score":0.4479755461215973},{"id":"https://openalex.org/C22648726","wikidata":"https://www.wikidata.org/wiki/Q7523744","display_name":"Single-linkage clustering","level":5,"score":0.440290629863739},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4138016700744629},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3849780857563019},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.3541101813316345},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3258393406867981},{"id":"https://openalex.org/C94641424","wikidata":"https://www.wikidata.org/wiki/Q5172845","display_name":"Correlation clustering","level":3,"score":0.298591673374176},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2177358865737915},{"id":"https://openalex.org/C33704608","wikidata":"https://www.wikidata.org/wiki/Q5014717","display_name":"CURE data clustering algorithm","level":4,"score":0.19292110204696655},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.18213453888893127},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.17750659584999084},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.06767198443412781},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1021/ci9801623","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci9801623","pdf_url":null,"source":{"id":"https://openalex.org/S171559003","display_name":"Journal of Chemical Information and Computer Sciences","issn_l":"0095-2338","issn":["0095-2338","1520-5142"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Computer Sciences","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Sustainable cities and communities","score":0.46000000834465027,"id":"https://metadata.un.org/sdg/11"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321040","display_name":"National Science Council","ror":"https://ror.org/02kv4zf79"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":14,"referenced_works":["https://openalex.org/W1247114292","https://openalex.org/W1493454437","https://openalex.org/W1592831460","https://openalex.org/W1973611342","https://openalex.org/W1990417739","https://openalex.org/W1991745348","https://openalex.org/W1992724796","https://openalex.org/W2030165149","https://openalex.org/W2037319728","https://openalex.org/W2089923519","https://openalex.org/W2103636724","https://openalex.org/W2142806163","https://openalex.org/W2162171655","https://openalex.org/W2311078281"],"related_works":["https://openalex.org/W1985101567","https://openalex.org/W2488882714","https://openalex.org/W2318830132","https://openalex.org/W126354040","https://openalex.org/W2959239999","https://openalex.org/W2979935139","https://openalex.org/W583850877","https://openalex.org/W2357582197","https://openalex.org/W1493637077","https://openalex.org/W2976247231"],"abstract_inverted_index":{"A":[0],"clustering":[1,14,131,147,179],"analysis":[2],"method":[3,132,173],"using":[4],"the":[5,41,46,102,111,159,162,172,177],"number":[6,33,42,84,163],"of":[7,19,34,43,45,53,55,63,71,73,85,104,107,128,138,164],"commonly":[8,35,86,165],"exposed":[9,36,87,166],"groups":[10,37,54,62,88,167],"identified":[11,39,89],"as":[12,40,68,79,158],"a":[13,17,93,118,136,142,145],"criterion":[15,121],"for":[16,61,122],"group":[18],"peptide":[20],"structures":[21,64,72],"generated":[22],"from":[23,141],"an":[24],"in":[25,151,161,181],"vacuo":[26],"molecular":[27],"dynamics":[28],"simulation":[29],"is":[30,38,133,174],"presented.":[31],"The":[32,126],"atoms":[44],"same":[47],"type":[48],"which":[49],"appear":[50],"on":[51],"vertices":[52],"three":[56],"dimensional":[57],"convex":[58],"hulls":[59],"computed":[60],"sampled":[65],"and":[66,144,184],"collected":[67],"blocks.":[69],"Blocks":[70],"high":[74],"structural":[75,153],"similarity":[76],"are":[77,90,99],"classified":[78],"clusters":[80],"if":[81],"their":[82],"corresponding":[83],"larger":[91],"than":[92],"preset":[94],"criterion.":[95],"Linkages":[96],"between":[97],"blocks":[98,105],"provided":[100],"with":[101],"generation":[103],"consisting":[106],"overlapping":[108],"structures.":[109],"However,":[110],"linkage":[112],"can":[113,155],"be":[114,156],"eliminated":[115],"by":[116],"employing":[117],"minimal":[119],"distance":[120],"each":[123],"block":[124],"generated.":[125],"feasibility":[127],"this":[129],"proposed":[130],"tested":[134],"through":[135],"comparison":[137],"results":[139],"obtained":[140],"conventional":[143,178],"hierarchical":[146],"method.":[148],"Since":[149],"change":[150,160],"fine":[152],"features":[154],"detected":[157],"identified,":[168],"we":[169],"find":[170],"that":[171],"superior":[175],"to":[176],"one":[180],"partitioning":[182],"compact":[183],"well-separated":[185],"clusters.":[186]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}