{"id":"https://openalex.org/W2150944048","doi":"https://doi.org/10.1186/s13015-015-0036-6","title":"Protein docking with predicted constraints","display_name":"Protein docking with predicted constraints","publication_year":2015,"publication_date":"2015-02-19","ids":{"openalex":"https://openalex.org/W2150944048","doi":"https://doi.org/10.1186/s13015-015-0036-6","mag":"2150944048","pmid":"https://pubmed.ncbi.nlm.nih.gov/25722738"},"language":"en","primary_location":{"id":"doi:10.1186/s13015-015-0036-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-015-0036-6","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-015-0036-6","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"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":"Algorithms for Molecular Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-015-0036-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5044582806","display_name":"Ludwig Krippahl","orcid":"https://orcid.org/0000-0002-3774-8624"},"institutions":[{"id":"https://openalex.org/I4210127031","display_name":"Uninova","ror":"https://ror.org/0373te416","country_code":"PT","type":"funder","lineage":["https://openalex.org/I4210127031"]}],"countries":["PT"],"is_corresponding":true,"raw_author_name":"Ludwig Krippahl","raw_affiliation_strings":["CENTRIA, Dept. Inform\u00e1tica, FCT, UNL, Caparica, 2829-516 Portugal","CENTRIA, Dept. Inform\u00e1tica, FCT, UNL, Caparica, 2829-516, Portugal"],"affiliations":[{"raw_affiliation_string":"CENTRIA, Dept. Inform\u00e1tica, FCT, UNL, Caparica, 2829-516 Portugal","institution_ids":["https://openalex.org/I4210127031"]},{"raw_affiliation_string":"CENTRIA, Dept. Inform\u00e1tica, FCT, UNL, Caparica, 2829-516, Portugal","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5077525447","display_name":"Pedro Barahona","orcid":"https://orcid.org/0000-0002-8355-4986"},"institutions":[{"id":"https://openalex.org/I4210127031","display_name":"Uninova","ror":"https://ror.org/0373te416","country_code":"PT","type":"funder","lineage":["https://openalex.org/I4210127031"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Pedro Barahona","raw_affiliation_strings":["CENTRIA, Dept. Inform\u00e1tica, FCT, UNL, Caparica, 2829-516 Portugal","CENTRIA, Dept. Inform\u00e1tica, FCT, UNL, Caparica, 2829-516, Portugal"],"affiliations":[{"raw_affiliation_string":"CENTRIA, Dept. Inform\u00e1tica, FCT, UNL, Caparica, 2829-516 Portugal","institution_ids":["https://openalex.org/I4210127031"]},{"raw_affiliation_string":"CENTRIA, Dept. Inform\u00e1tica, FCT, UNL, Caparica, 2829-516, Portugal","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5044582806"],"corresponding_institution_ids":["https://openalex.org/I4210127031"],"apc_list":{"value":1490,"currency":"GBP","value_usd":1827},"apc_paid":{"value":1490,"currency":"GBP","value_usd":1827},"fwci":0.6025,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.69447252,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"10","issue":"1","first_page":"9","last_page":"9"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9993000030517578,"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":0.9993000030517578,"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/T13326","display_name":"Biochemical and Structural Characterization","score":0.996399998664856,"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/T11124","display_name":"Protein purification and stability","score":0.9961000084877014,"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/computer-science","display_name":"Computer science","score":0.7426260709762573},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.6619979739189148},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.502549409866333},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4334872364997864},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.43280211091041565},{"id":"https://openalex.org/keywords/classifier","display_name":"Classifier (UML)","score":0.4320542812347412},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.30853521823883057}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7426260709762573},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.6619979739189148},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.502549409866333},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4334872364997864},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.43280211091041565},{"id":"https://openalex.org/C95623464","wikidata":"https://www.wikidata.org/wiki/Q1096149","display_name":"Classifier (UML)","level":2,"score":0.4320542812347412},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.30853521823883057},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/s13015-015-0036-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-015-0036-6","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-015-0036-6","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"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":"Algorithms for Molecular Biology","raw_type":"journal-article"},{"id":"pmid:25722738","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25722738","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":"Algorithms for molecular biology : AMB","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:4340843","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4340843","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms Mol Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13015-015-0036-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-015-0036-6","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-015-0036-6","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"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":"Algorithms for Molecular Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2150944048.pdf","grobid_xml":"https://content.openalex.org/works/W2150944048.grobid-xml"},"referenced_works_count":40,"referenced_works":["https://openalex.org/W15827419","https://openalex.org/W1506806321","https://openalex.org/W1532325895","https://openalex.org/W1571550538","https://openalex.org/W1585335141","https://openalex.org/W1663973292","https://openalex.org/W1968555047","https://openalex.org/W1974596630","https://openalex.org/W1993951624","https://openalex.org/W2004575181","https://openalex.org/W2008545402","https://openalex.org/W2012104865","https://openalex.org/W2022284509","https://openalex.org/W2025120281","https://openalex.org/W2027403155","https://openalex.org/W2055043387","https://openalex.org/W2064383522","https://openalex.org/W2076048958","https://openalex.org/W2091734240","https://openalex.org/W2092006899","https://openalex.org/W2093945918","https://openalex.org/W2101942831","https://openalex.org/W2117480021","https://openalex.org/W2127322768","https://openalex.org/W2130920760","https://openalex.org/W2130949063","https://openalex.org/W2134801216","https://openalex.org/W2137167381","https://openalex.org/W2137321308","https://openalex.org/W2141330566","https://openalex.org/W2153983456","https://openalex.org/W2158714788","https://openalex.org/W2159195671","https://openalex.org/W2165531467","https://openalex.org/W2487140311","https://openalex.org/W2550120957","https://openalex.org/W2578150941","https://openalex.org/W2915344963","https://openalex.org/W2970523279","https://openalex.org/W4213009331"],"related_works":["https://openalex.org/W2051487156","https://openalex.org/W2073681303","https://openalex.org/W2544423928","https://openalex.org/W2053286651","https://openalex.org/W2181743346","https://openalex.org/W2575434942","https://openalex.org/W2187401768","https://openalex.org/W2047838177","https://openalex.org/W2181413294","https://openalex.org/W2052122378"],"abstract_inverted_index":{"This":[0,40],"paper":[1],"presents":[2],"a":[3,31,46,82,123],"constraint-based":[4],"method":[5],"for":[6,21,56,85,117],"improving":[7],"protein":[8,149],"docking":[9,150,156],"results.":[10],"Efficient":[11],"constraint":[12],"propagation":[13],"cuts":[14],"over":[15],"95%":[16],"of":[17,49,139,148,169],"the":[18,23,26,54,136,144,170],"search":[19],"time":[20],"finding":[22],"configurations":[24],"with":[25,122,153],"largest":[27],"contact":[28,32,58,68,78],"surface,":[29],"provided":[30],"is":[33,93,114,129,164],"specified":[34],"between":[35],"two":[36],"amino":[37],"acid":[38],"residues.":[39],"makes":[41,97],"it":[42,98,128],"possible":[43],"to":[44,90,100,106,132],"scan":[45],"large":[47],"number":[48,138],"potentially":[50],"correct":[51,77],"constraints,":[52],"lowering":[53],"requirements":[55],"useful":[57],"predictions.":[59],"While":[60],"other":[61],"approaches":[62],"are":[63],"very":[64],"dependent":[65],"on":[66],"accurate":[67,130],"predictions,":[69],"ours":[70],"requires":[71],"only":[72],"that":[73,96,127],"at":[74],"least":[75],"one":[76,87],"be":[79],"retained":[80,142],"in":[81,161],"set":[83],"of,":[84],"example,":[86],"hundred":[88],"constraints":[89],"test.":[91],"It":[92],"this":[94,162],"feature":[95],"feasible":[99],"use":[101],"readily":[102],"available":[103,166],"sequence":[104],"data":[105],"predict":[107],"specific":[108],"potential":[109],"contacts.":[110],"Although":[111],"such":[112],"prediction":[113],"too":[115],"inaccurate":[116],"most":[118],"purposes,":[119],"we":[120],"demonstrate":[121],"Na\u00efve":[124],"Bayes":[125],"Classifier":[126],"enough":[131],"more":[133],"than":[134],"double":[135],"average":[137],"acceptable":[140],"models":[141],"during":[143],"crucial":[145],"filtering":[146],"stage":[147],"when":[151],"combined":[152],"our":[154],"constrained":[155],"algorithm.":[157],"All":[158],"software":[159],"developed":[160],"work":[163],"freely":[165],"as":[167],"part":[168],"Open":[171],"Chemera":[172],"Library.":[173]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
