{"id":"https://openalex.org/W2216240350","doi":"https://doi.org/10.1109/bibm.2015.7359858","title":"Predicting protein-ligand binding specificity based on ensemble clustering","display_name":"Predicting protein-ligand binding specificity based on ensemble clustering","publication_year":2015,"publication_date":"2015-11-01","ids":{"openalex":"https://openalex.org/W2216240350","doi":"https://doi.org/10.1109/bibm.2015.7359858","mag":"2216240350"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2015.7359858","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2015.7359858","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-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/A5022946654","display_name":"Ziyi Guo","orcid":"https://orcid.org/0000-0002-7481-0140"},"institutions":[{"id":"https://openalex.org/I186143895","display_name":"Lehigh University","ror":"https://ror.org/012afjb06","country_code":"US","type":"education","lineage":["https://openalex.org/I186143895"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ziyi Guo","raw_affiliation_strings":["Dept. of Computer Science and Engineering, Lehigh University, Bethlehem, PA, USA"],"affiliations":[{"raw_affiliation_string":"Dept. of Computer Science and Engineering, Lehigh University, Bethlehem, PA, USA","institution_ids":["https://openalex.org/I186143895"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062182398","display_name":"Brian Y. Chen","orcid":"https://orcid.org/0000-0001-9025-0107"},"institutions":[{"id":"https://openalex.org/I186143895","display_name":"Lehigh University","ror":"https://ror.org/012afjb06","country_code":"US","type":"education","lineage":["https://openalex.org/I186143895"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brian Y. Chen","raw_affiliation_strings":["Dept. of Computer Science and Engineering, Lehigh University, Bethlehem, PA, USA"],"affiliations":[{"raw_affiliation_string":"Dept. of Computer Science and Engineering, Lehigh University, Bethlehem, PA, USA","institution_ids":["https://openalex.org/I186143895"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5022946654"],"corresponding_institution_ids":["https://openalex.org/I186143895"],"apc_list":null,"apc_paid":null,"fwci":0.1459,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.56310866,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"7","issue":null,"first_page":"1239","last_page":"1245"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9998000264167786,"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":0.9998000264167786,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9991999864578247,"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/binding-site","display_name":"Binding site","score":0.5707271695137024},{"id":"https://openalex.org/keywords/conformational-ensembles","display_name":"Conformational ensembles","score":0.5137611627578735},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.47855788469314575},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.47574707865715027},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.435110479593277},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.39240074157714844},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.33831512928009033},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.26847127079963684},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2615259289741516},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.17851954698562622}],"concepts":[{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.5707271695137024},{"id":"https://openalex.org/C2777936996","wikidata":"https://www.wikidata.org/wiki/Q17148461","display_name":"Conformational ensembles","level":3,"score":0.5137611627578735},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.47855788469314575},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.47574707865715027},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.435110479593277},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.39240074157714844},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.33831512928009033},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.26847127079963684},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2615259289741516},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.17851954698562622}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm.2015.7359858","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2015.7359858","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":49,"referenced_works":["https://openalex.org/W255996521","https://openalex.org/W605727707","https://openalex.org/W1510161841","https://openalex.org/W1544453230","https://openalex.org/W1604281503","https://openalex.org/W1933777541","https://openalex.org/W1965907701","https://openalex.org/W1965910641","https://openalex.org/W1966078827","https://openalex.org/W1967538863","https://openalex.org/W1976881268","https://openalex.org/W1978498560","https://openalex.org/W1990495809","https://openalex.org/W1993279060","https://openalex.org/W1997238096","https://openalex.org/W2002419486","https://openalex.org/W2003610577","https://openalex.org/W2005153862","https://openalex.org/W2021081942","https://openalex.org/W2023790301","https://openalex.org/W2033536765","https://openalex.org/W2036987424","https://openalex.org/W2037913468","https://openalex.org/W2038441393","https://openalex.org/W2049905965","https://openalex.org/W2051895548","https://openalex.org/W2056248536","https://openalex.org/W2056333944","https://openalex.org/W2059013803","https://openalex.org/W2075805421","https://openalex.org/W2077776336","https://openalex.org/W2081492752","https://openalex.org/W2081693079","https://openalex.org/W2082115790","https://openalex.org/W2093425004","https://openalex.org/W2110401277","https://openalex.org/W2130479394","https://openalex.org/W2138770756","https://openalex.org/W2142598588","https://openalex.org/W2148823738","https://openalex.org/W2152326664","https://openalex.org/W2168964504","https://openalex.org/W2411160307","https://openalex.org/W4229791580","https://openalex.org/W4232478844","https://openalex.org/W4236653231","https://openalex.org/W6609701964","https://openalex.org/W6649793018","https://openalex.org/W6659924431"],"related_works":["https://openalex.org/W2059608951","https://openalex.org/W2013298251","https://openalex.org/W2914759153","https://openalex.org/W4292636432","https://openalex.org/W4294957617","https://openalex.org/W1951660422","https://openalex.org/W1991917050","https://openalex.org/W4387012733","https://openalex.org/W2883121577","https://openalex.org/W2107100645"],"abstract_inverted_index":{"Protein":[0],"structure":[1],"comparison":[2],"algorithms":[3],"can":[4,29,74,146],"be":[5],"used":[6],"to":[7,13,111],"identify":[8],"distantly":[9,26],"related":[10,27],"proteins":[11,28,148],"or":[12],"categorize":[14],"differences":[15],"in":[16,23,101,120,153],"binding":[17,76,80,96,103,116,124,151,158],"specificities.":[18],"When":[19],"they":[20,51],"are":[21,39],"presented":[22],"different":[24],"conformations,":[25],"go":[30],"unrecognized":[31],"unless":[32],"flexible":[33],"representations":[34,42],"of":[35,47,58,115,123,134,156],"whole":[36],"protein":[37,95,132],"structures":[38],"used.":[40],"Such":[41],"offer":[43],"a":[44,91],"sophisticated":[45],"description":[46],"backbone":[48],"motion,":[49],"but":[50],"do":[52],"not":[53],"incorporate":[54,112],"the":[55,102,113,129,154],"potential":[56],"motion":[57],"every":[59],"atom.":[60],"Thus,":[61],"existing":[62],"representations,":[63],"both":[64],"rigid":[65],"and":[66,137],"flexible,":[67],"cannot":[68],"compensate":[69],"for":[70,93],"atomic":[71],"motions":[72],"that":[73,143],"make":[75],"sites":[77,97],"with":[78,149],"similar":[79,150],"preferences":[81,152],"appear":[82],"different.":[83],"To":[84],"bridge":[85],"this":[86,88,144],"gap,":[87],"paper":[89],"presents":[90],"tool":[92],"comparing":[94],"despite":[98],"conformational":[99,121],"changes":[100],"site.":[104],"Our":[105,140],"method":[106,130],"employs":[107],"ensemble":[108],"clustering":[109],"techniques":[110],"diversity":[114],"site":[117,125,159],"variations":[118],"observed":[119],"samples":[122],"motion.":[126],"We":[127],"applied":[128],"on":[131],"conformations":[133],"serine":[135],"proteases":[136],"enolase":[138],"superfamilies.":[139],"results":[141],"demonstrate":[142],"approach":[145],"distinguish":[147],"presence":[155],"considerable":[157],"flexibility.":[160]},"counts_by_year":[{"year":2016,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
