{"id":"https://openalex.org/W185786443","doi":"https://doi.org/10.1186/1758-2946-4-s1-p35","title":"Development of target-biased scoring functions for protein-ligand docking","display_name":"Development of target-biased scoring functions for protein-ligand docking","publication_year":2012,"publication_date":"2012-05-01","ids":{"openalex":"https://openalex.org/W185786443","doi":"https://doi.org/10.1186/1758-2946-4-s1-p35","mag":"185786443"},"language":"en","primary_location":{"id":"doi:10.1186/1758-2946-4-s1-p35","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-4-s1-p35","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-4-S1-P35","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"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":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-4-S1-P35","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5038969460","display_name":"Michael Scharfe","orcid":null},"institutions":[{"id":"https://openalex.org/I18860807","display_name":"Wittenberg University","ror":"https://ror.org/04a23br85","country_code":"US","type":"education","lineage":["https://openalex.org/I18860807"]},{"id":"https://openalex.org/I68956291","display_name":"Martin Luther University Halle-Wittenberg","ror":"https://ror.org/05gqaka33","country_code":"DE","type":"education","lineage":["https://openalex.org/I68956291"]}],"countries":["DE","US"],"is_corresponding":true,"raw_author_name":"Michael Scharfe","raw_affiliation_strings":["Institute of Pharmacy, Pharmaceutical Chemistry, University Halle-Wittenberg, Halle, 06120, Germany","Institute of Pharmacy, Pharmaceutical Chemistry, University Halle-Wittenberg, Halle, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Pharmacy, Pharmaceutical Chemistry, University Halle-Wittenberg, Halle, 06120, Germany","institution_ids":["https://openalex.org/I18860807","https://openalex.org/I68956291"]},{"raw_affiliation_string":"Institute of Pharmacy, Pharmaceutical Chemistry, University Halle-Wittenberg, Halle, Germany","institution_ids":["https://openalex.org/I68956291"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085636203","display_name":"Martin Pippel","orcid":"https://orcid.org/0000-0002-8134-5929"},"institutions":[{"id":"https://openalex.org/I18860807","display_name":"Wittenberg University","ror":"https://ror.org/04a23br85","country_code":"US","type":"education","lineage":["https://openalex.org/I18860807"]},{"id":"https://openalex.org/I68956291","display_name":"Martin Luther University Halle-Wittenberg","ror":"https://ror.org/05gqaka33","country_code":"DE","type":"education","lineage":["https://openalex.org/I68956291"]}],"countries":["DE","US"],"is_corresponding":false,"raw_author_name":"Martin Pippel","raw_affiliation_strings":["Institute of Pharmacy, Pharmaceutical Chemistry, University Halle-Wittenberg, Halle, 06120, Germany","Institute of Pharmacy, Pharmaceutical Chemistry, University Halle-Wittenberg, Halle, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Pharmacy, Pharmaceutical Chemistry, University Halle-Wittenberg, Halle, 06120, Germany","institution_ids":["https://openalex.org/I18860807","https://openalex.org/I68956291"]},{"raw_affiliation_string":"Institute of Pharmacy, Pharmaceutical Chemistry, University Halle-Wittenberg, Halle, Germany","institution_ids":["https://openalex.org/I68956291"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5055328126","display_name":"Wolfgang Sippl","orcid":"https://orcid.org/0000-0002-5985-9261"},"institutions":[{"id":"https://openalex.org/I18860807","display_name":"Wittenberg University","ror":"https://ror.org/04a23br85","country_code":"US","type":"education","lineage":["https://openalex.org/I18860807"]},{"id":"https://openalex.org/I68956291","display_name":"Martin Luther University Halle-Wittenberg","ror":"https://ror.org/05gqaka33","country_code":"DE","type":"education","lineage":["https://openalex.org/I68956291"]}],"countries":["DE","US"],"is_corresponding":false,"raw_author_name":"Wolfgang Sippl","raw_affiliation_strings":["Institute of Pharmacy, Pharmaceutical Chemistry, University Halle-Wittenberg, Halle, 06120, Germany","Institute of Pharmacy, Pharmaceutical Chemistry, University Halle-Wittenberg, Halle, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Pharmacy, Pharmaceutical Chemistry, University Halle-Wittenberg, Halle, 06120, Germany","institution_ids":["https://openalex.org/I18860807","https://openalex.org/I68956291"]},{"raw_affiliation_string":"Institute of Pharmacy, Pharmaceutical Chemistry, University Halle-Wittenberg, Halle, Germany","institution_ids":["https://openalex.org/I68956291"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5038969460"],"corresponding_institution_ids":["https://openalex.org/I18860807","https://openalex.org/I68956291"],"apc_list":{"value":2190,"currency":"USD","value_usd":2190},"apc_paid":{"value":2190,"currency":"USD","value_usd":2190},"fwci":0.0,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.00965629,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":96},"biblio":{"volume":"4","issue":"S1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9790999889373779,"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/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.9718000292778015,"subfield":{"id":"https://openalex.org/subfields/2736","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.8412314653396606},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7049009799957275},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.5945824980735779},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5767170190811157},{"id":"https://openalex.org/keywords/random-forest","display_name":"Random forest","score":0.5255290865898132},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5229447484016418},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.49085456132888794},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.46049264073371887},{"id":"https://openalex.org/keywords/protein\u2013ligand-docking","display_name":"Protein\u2013ligand docking","score":0.45034003257751465},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4415053427219391},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.24951708316802979},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.21072492003440857}],"concepts":[{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.8412314653396606},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7049009799957275},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.5945824980735779},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5767170190811157},{"id":"https://openalex.org/C169258074","wikidata":"https://www.wikidata.org/wiki/Q245748","display_name":"Random forest","level":2,"score":0.5255290865898132},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5229447484016418},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.49085456132888794},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.46049264073371887},{"id":"https://openalex.org/C77319485","wikidata":"https://www.wikidata.org/wiki/Q7251520","display_name":"Protein\u2013ligand docking","level":4,"score":0.45034003257751465},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4415053427219391},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.24951708316802979},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.21072492003440857},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.0},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","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},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/1758-2946-4-s1-p35","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-4-s1-p35","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-4-S1-P35","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"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":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3341274","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3341274","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":"J Cheminform","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:59789615cda54cfd8fa60aed6e477753","is_oa":true,"landing_page_url":"https://doaj.org/article/59789615cda54cfd8fa60aed6e477753","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":"Journal of Cheminformatics, Vol 4, Iss Suppl 1, p P35 (2012)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/1758-2946-4-s1-p35","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-4-s1-p35","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-4-S1-P35","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"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":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W185786443.pdf","grobid_xml":"https://content.openalex.org/works/W185786443.grobid-xml"},"referenced_works_count":2,"referenced_works":["https://openalex.org/W2001722230","https://openalex.org/W2087256237"],"related_works":["https://openalex.org/W1581147483","https://openalex.org/W4310018788","https://openalex.org/W2329052364","https://openalex.org/W2417162538","https://openalex.org/W2162967120","https://openalex.org/W2057846043","https://openalex.org/W2336040088","https://openalex.org/W2027065525","https://openalex.org/W2773493604","https://openalex.org/W2269591907"],"abstract_inverted_index":{"Accurate":[0],"scoring":[1,23,40,98,101,133,169,200,242,259],"of":[2,21,38,80,86,240],"protein-ligand":[3,120,128,201],"interactions":[4],"for":[5,74,127,148,167,199,256],"docking,":[6,129],"binding-affinity":[7],"prediction":[8],"and":[9,42,52,171,206,252,258],"virtual":[10,75],"screening":[11],"campaigns":[12],"is":[13,56,83,185,221],"still":[14],"challenging.":[15],"Despite":[16],"great":[17],"efforts,":[18],"the":[19,28,36,78,84,90,168,192],"performance":[20,47],"existing":[22],"functions":[24,102,243],"strongly":[25],"depends":[26],"on":[27,105,213],"target":[29,225,250],"structure":[30],"under":[31],"investigation.":[32],"Recent":[33],"developments":[34],"in":[35,49,113,218],"direction":[37],"target-class-specific":[39,97],"methods":[41,161],"machine-learning-based":[43],"procedures":[44,190],"reveal":[45],"significant":[46],"improvement":[48],"binding":[50,175],"mode":[51],"affinity":[53],"prediction.\r\n\r\nHowever,":[54],"there":[55],"no":[57],"open-source":[58,91],"framework":[59,92,194],"that":[60,142,177,244],"combines":[61],"such":[62],"sophisticated":[63],"techniques":[64],"with":[65,227],"molecular":[66],"docking":[67,257],"algorithms":[68,126],"to":[69,95,118,180,186,195,223,236,247],"make":[70],"them":[71],"simply":[72],"applicable":[73,222],"screening.":[76],"Therefore,":[77],"aim":[79],"this":[81,211],"work":[82],"implementation":[85],"general":[87],"tools":[88],"within":[89,191,260],"ParaDockS":[93,123,193],"[1]":[94],"obtain":[96,237],"functions.":[99],"These":[100],"are":[103,145,178,245],"based":[104],"knowledge-based":[106],"atom-pair":[107,143],"potentials":[108,144],"which":[109],"can":[110,135,253],"be":[111,136,254],"used":[112,255],"an":[114],"additive":[115],"manner":[116],"(PMF-Score)":[117],"score":[119],"complexes.":[121],"Because":[122],"already":[124],"includes":[125],"every":[130,224],"new":[131],"obtained":[132],"function":[134,170],"immediately":[137],"applied.\r\n\r\nRecently":[138],"it":[139,220],"was":[140],"shown,":[141],"also":[146],"useful":[147],"training":[149],"machine-learning":[150,189],"models":[151],"like":[152],"support":[153],"vector":[154],"machines":[155],"or":[156],"random":[157],"forests":[158],"[2].":[159],"Such":[160],"circumvent":[162],"a":[163,203,238,248],"particular":[164],"functional":[165],"form":[166],"thereby":[172],"implicitly":[173],"capture":[174],"contributions":[176],"hard":[179],"model":[181],"explicitly.":[182],"Our":[183],"goal":[184],"implement":[187],"different":[188,241],"provide":[196],"further":[197,232],"possibilities":[198],"complexes.\r\n\r\nIn":[202],"first":[204],"test":[205],"validation":[207],"study,":[208],"we":[209,234],"applied":[210],"workflow":[212],"kinase":[214],"data":[215],"sets,":[216],"but":[217],"principle":[219],"class":[226,251],"enough":[228],"structural":[229],"data.":[230],"In":[231],"studies":[233],"want":[235],"set":[239],"biased":[246],"certain":[249],"ParaDockS.":[261]},"counts_by_year":[{"year":2016,"cited_by_count":2}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2016-06-24T00:00:00"}
