{"id":"https://openalex.org/W2077199786","doi":"https://doi.org/10.1186/1471-2105-11-236","title":"Analysis of protein-protein docking decoys using interaction fingerprints: application to the reconstruction of CaM-ligand complexes","display_name":"Analysis of protein-protein docking decoys using interaction fingerprints: application to the reconstruction of CaM-ligand complexes","publication_year":2010,"publication_date":"2010-05-11","ids":{"openalex":"https://openalex.org/W2077199786","doi":"https://doi.org/10.1186/1471-2105-11-236","mag":"2077199786","pmid":"https://pubmed.ncbi.nlm.nih.gov/20459766"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-11-236","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-236","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-236","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-236","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5081689180","display_name":"Nobuyuki Uchikoga","orcid":null},"institutions":[{"id":"https://openalex.org/I4210104082","display_name":"Japan Biological Informatics Consortium","ror":"https://ror.org/01astg473","country_code":"JP","type":"nonprofit","lineage":["https://openalex.org/I4210104082"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Nobuyuki Uchikoga","raw_affiliation_strings":["Japan Biological Informatics Consortium, 2-45 Aomi, Koto-ku, Tokyo, Japan. n.uchikoga@aist.go.jp","Japan Biological Informatics Consortium, 2-45 Aomi, Koto-ku, Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Japan Biological Informatics Consortium, 2-45 Aomi, Koto-ku, Tokyo, Japan. n.uchikoga@aist.go.jp","institution_ids":["https://openalex.org/I4210104082"]},{"raw_affiliation_string":"Japan Biological Informatics Consortium, 2-45 Aomi, Koto-ku, Tokyo, Japan","institution_ids":["https://openalex.org/I4210104082"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027918582","display_name":"Takatsugu Hirokawa","orcid":"https://orcid.org/0000-0002-3180-5050"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Takatsugu Hirokawa","raw_affiliation_strings":["Computational Biology Research Center, Advanced Industrial Science and Technology, 2-42 Aomi, Koto-ku, Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biology Research Center, Advanced Industrial Science and Technology, 2-42 Aomi, Koto-ku, Tokyo, Japan","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5027918582","https://openalex.org/A5081689180"],"corresponding_institution_ids":["https://openalex.org/I4210104082"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.6226,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.66637047,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"11","issue":"1","first_page":"236","last_page":"236"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12030","display_name":"S100 Proteins and Annexins","score":0.09390000253915787,"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/T12030","display_name":"S100 Proteins and Annexins","score":0.09390000253915787,"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/T10086","display_name":"Alzheimer's disease research and treatments","score":0.0722000002861023,"subfield":{"id":"https://openalex.org/subfields/2737","display_name":"Physiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T13127","display_name":"Biotin and Related Studies","score":0.06459999829530716,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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/docking","display_name":"Docking (animal)","score":0.8059660196304321},{"id":"https://openalex.org/keywords/protein\u2013ligand-docking","display_name":"Protein\u2013ligand docking","score":0.6921378374099731},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6497557163238525},{"id":"https://openalex.org/keywords/protein-ligand","display_name":"Protein ligand","score":0.4642098546028137},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.4495691657066345},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4257934093475342},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3798731863498688},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3384784758090973},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.3194159269332886},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2662404775619507},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.2553717792034149},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.2189502716064453},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.12486568093299866}],"concepts":[{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.8059660196304321},{"id":"https://openalex.org/C77319485","wikidata":"https://www.wikidata.org/wiki/Q7251520","display_name":"Protein\u2013ligand docking","level":4,"score":0.6921378374099731},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6497557163238525},{"id":"https://openalex.org/C109095088","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Protein ligand","level":2,"score":0.4642098546028137},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.4495691657066345},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4257934093475342},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3798731863498688},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3384784758090973},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.3194159269332886},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2662404775619507},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.2553717792034149},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.2189502716064453},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.12486568093299866},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002147","descriptor_name":"Calmodulin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002147","descriptor_name":"Calmodulin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002147","descriptor_name":"Calmodulin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009682","descriptor_name":"Magnetic Resonance Spectroscopy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009682","descriptor_name":"Magnetic Resonance Spectroscopy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009682","descriptor_name":"Magnetic Resonance Spectroscopy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D046912","descriptor_name":"Multiprotein Complexes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D046912","descriptor_name":"Multiprotein Complexes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D046912","descriptor_name":"Multiprotein Complexes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D046912","descriptor_name":"Multiprotein Complexes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D046912","descriptor_name":"Multiprotein Complexes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D046912","descriptor_name":"Multiprotein Complexes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-11-236","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-236","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-236","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:20459766","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20459766","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:67e6cf43be744c44b2592e5a9315cdb9","is_oa":true,"landing_page_url":"https://doaj.org/article/67e6cf43be744c44b2592e5a9315cdb9","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 11, Iss 1, p 236 (2010)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2873953","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2873953","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-11-236","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-236","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-236","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6299999952316284,"id":"https://metadata.un.org/sdg/10","display_name":"Reduced inequalities"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2077199786.pdf","grobid_xml":"https://content.openalex.org/works/W2077199786.grobid-xml"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W1576403707","https://openalex.org/W1965457996","https://openalex.org/W1975121208","https://openalex.org/W1980389409","https://openalex.org/W2001535102","https://openalex.org/W2009129583","https://openalex.org/W2015403140","https://openalex.org/W2018410079","https://openalex.org/W2029870632","https://openalex.org/W2048803110","https://openalex.org/W2059975159","https://openalex.org/W2070724962","https://openalex.org/W2081912151","https://openalex.org/W2083995470","https://openalex.org/W2094174735","https://openalex.org/W2094493457","https://openalex.org/W2110483430","https://openalex.org/W2115190629","https://openalex.org/W2118542302","https://openalex.org/W2129454543","https://openalex.org/W2130790725","https://openalex.org/W2133712572","https://openalex.org/W2133842820","https://openalex.org/W2143482176","https://openalex.org/W2144885342","https://openalex.org/W2168045053","https://openalex.org/W2169085737","https://openalex.org/W3103786587"],"related_works":["https://openalex.org/W1581147483","https://openalex.org/W2329052364","https://openalex.org/W4310018788","https://openalex.org/W2417162538","https://openalex.org/W2162967120","https://openalex.org/W4308805210","https://openalex.org/W2005817231","https://openalex.org/W2331956508","https://openalex.org/W2885308902","https://openalex.org/W2031553931"],"abstract_inverted_index":{"BACKGROUND:":[0],"Protein-protein":[1],"docking":[2,45,60,146,212],"for":[3,19,27,42,80,210],"proteins":[4],"with":[5,61],"large":[6,48],"conformational":[7,49],"changes":[8,50],"was":[9],"analyzed":[10,163],"by":[11,46],"using":[12,71,164],"interaction":[13,72,165,182,205],"fingerprints,":[14],"one":[15],"of":[16,57,66,83,96,102,113,176,214],"the":[17,81,93,100,110,123,145,149,159,174,190,204],"scales":[18],"measuring":[20],"similarities":[21,157],"among":[22],"complex":[23,33,161],"structures,":[24,64],"utilized":[25],"especially":[26],"searching":[28],"near-native":[29,186],"protein-ligand":[30],"or":[31],"protein-protein":[32,44,211],"structures.":[34],"Here,":[35],"we":[36,104],"have":[37],"proposed":[38],"a":[39,199],"combined":[40,54,85,200],"method":[41,55,184,192,201],"analyzing":[43],"taking":[47],"into":[51],"consideration.":[52],"This":[53],"consists":[56],"ensemble":[58],"soft":[59],"multiple":[62],"protein":[63],"refinement":[65],"complexes,":[67],"and":[68,74,122,130,148,155,167,178],"cluster":[69,194],"analysis":[70,213],"fingerprints":[73],"energy":[75,153],"profiles.":[76],"RESULTS:":[77],"To":[78],"test":[79],"applicability":[82],"this":[84],"method,":[86],"various":[87],"CaM-ligand":[88,140],"complexes":[89,141],"were":[90,142,162,171],"reconstructed":[91],"from":[92],"NMR":[94],"structures":[95,187],"unbound":[97],"CaM.":[98],"For":[99,136],"purpose":[101],"reconstruction,":[103],"used":[105],"three":[106],"known":[107],"CaM-ligands,":[108],"namely,":[109],"CaM-binding":[111],"peptides":[112],"cyclic":[114],"nucleotide":[115],"gateway":[116],"(CNG),":[117],"CaM":[118,134],"kinase":[119,120],"(CaMKK)":[121],"plasma":[124],"membrane":[125],"Ca2+":[126],"ATPase":[127],"pump":[128],"(PMCA),":[129],"thirty-one":[131],"structurally":[132],"diverse":[133],"conformations.":[135],"each":[137],"ligand,":[138],"62000":[139],"generated":[143],"in":[144,173,193],"step":[147],"relationship":[150],"between":[151],"their":[152],"profiles":[154],"structural":[156],"to":[158],"native":[160],"fingerprint":[166,183,206],"RMSD.":[168],"Near-native":[169],"clusters":[170],"obtained":[172],"case":[175],"CNG":[177],"CaMKK.":[179],"CONCLUSIONS:":[180],"The":[181],"discriminated":[185],"better":[188],"than":[189],"RMSD":[191],"analysis.":[195],"We":[196],"showed":[197],"that":[198,202],"includes":[203],"is":[207],"very":[208],"useful":[209],"certain":[215],"cases.":[216]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":1}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}
