{"id":"https://openalex.org/W2128809549","doi":"https://doi.org/10.1186/1758-2946-3-s1-p35","title":"PARADOCKS \u2013 a framework for molecular docking","display_name":"PARADOCKS \u2013 a framework for molecular docking","publication_year":2011,"publication_date":"2011-04-19","ids":{"openalex":"https://openalex.org/W2128809549","doi":"https://doi.org/10.1186/1758-2946-3-s1-p35","mag":"2128809549"},"language":"en","primary_location":{"id":"doi:10.1186/1758-2946-3-s1-p35","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-3-s1-p35","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-3-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/track/pdf/10.1186/1758-2946-3-S1-P35","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5085636203","display_name":"Martin Pippel","orcid":"https://orcid.org/0000-0002-8134-5929"},"institutions":[{"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"],"is_corresponding":true,"raw_author_name":"M Pippel","raw_affiliation_strings":["Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, 06120, Halle (Saale), Germany","Institute of Pharmacy, Martin Luther University of Halle\u2010Wittenberg  Halle/Saale Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, 06120, Halle (Saale), Germany","institution_ids":["https://openalex.org/I68956291"]},{"raw_affiliation_string":"Institute of Pharmacy, Martin Luther University of Halle\u2010Wittenberg  Halle/Saale Germany","institution_ids":["https://openalex.org/I68956291"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036790593","display_name":"Ren\u00e9 Meier","orcid":"https://orcid.org/0000-0002-1501-1349"},"institutions":[{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"R Meier","raw_affiliation_strings":["Institute of Biochemistry, University of Leipzig, 04103, Leipzig, Germany","Institute of Biochemistry, University of Leipzig Leipzig Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biochemistry, University of Leipzig, 04103, Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]},{"raw_affiliation_string":"Institute of Biochemistry, University of Leipzig Leipzig Germany","institution_ids":["https://openalex.org/I926574661"]}]},{"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/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"],"is_corresponding":false,"raw_author_name":"W Sippl","raw_affiliation_strings":["Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, 06120, Halle (Saale), Germany","Institute of Pharmacy, Martin Luther University of Halle\u2010Wittenberg  Halle/Saale Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, 06120, Halle (Saale), Germany","institution_ids":["https://openalex.org/I68956291"]},{"raw_affiliation_string":"Institute of Pharmacy, Martin Luther University of Halle\u2010Wittenberg  Halle/Saale Germany","institution_ids":["https://openalex.org/I68956291"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5085636203"],"corresponding_institution_ids":["https://openalex.org/I68956291"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":0.0,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.16420205,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"3","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":0.9886999726295471,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.9811000227928162,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6153151988983154},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.5102658271789551},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.48893895745277405},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3781183958053589},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3501327335834503},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.1569368839263916},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11739930510520935}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6153151988983154},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.5102658271789551},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.48893895745277405},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3781183958053589},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3501327335834503},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.1569368839263916},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11739930510520935},{"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:10.1186/1758-2946-3-s1-p35","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-3-s1-p35","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-3-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:doaj.org/article:5157de47939f4a2eb868854c93d2255d","is_oa":false,"landing_page_url":"https://doaj.org/article/5157de47939f4a2eb868854c93d2255d","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 3, Iss Suppl 1, p P35 (2011)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2091971","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3083591","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1758-2946-3-s1-p35","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-3-s1-p35","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-3-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":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2128809549.pdf","grobid_xml":"https://content.openalex.org/works/W2128809549.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W83502394","https://openalex.org/W1483621455","https://openalex.org/W1567411871","https://openalex.org/W1577668191","https://openalex.org/W1605578858","https://openalex.org/W1656114533","https://openalex.org/W1970651561","https://openalex.org/W1983194490","https://openalex.org/W1988437166","https://openalex.org/W1990472384","https://openalex.org/W2003356525","https://openalex.org/W2015461838","https://openalex.org/W2015907087","https://openalex.org/W2019750793","https://openalex.org/W2027640169","https://openalex.org/W2061079400","https://openalex.org/W2067455153","https://openalex.org/W2068489657","https://openalex.org/W2068672372","https://openalex.org/W2087256237","https://openalex.org/W2092285329","https://openalex.org/W2107506448","https://openalex.org/W2114779636","https://openalex.org/W2114819818","https://openalex.org/W2118512515","https://openalex.org/W2127760066","https://openalex.org/W2128332459","https://openalex.org/W2135732933","https://openalex.org/W2135817448","https://openalex.org/W2142334951","https://openalex.org/W2147774191","https://openalex.org/W2158360182","https://openalex.org/W2158534713","https://openalex.org/W2543580944"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2382290278","https://openalex.org/W2350741829","https://openalex.org/W2130043461","https://openalex.org/W2530322880","https://openalex.org/W1596801655"],"abstract_inverted_index":{"The":[0,177],"prediction":[1],"of":[2,10,21,51,75,111,127,183,194,216,224,232],"possible":[3],"binding":[4,16],"geometries":[5],"as":[6,8],"well":[7],"ranking":[9],"putative":[11],"protein-ligand":[12],"complexes":[13,29],"according":[14],"their":[15,152],"affinities":[17],"is":[18,95,163,166,180],"the":[19,48,64,70,73,76,85,109,112,118,123,144,181,190,192,202,214,237],"intention":[20],"so":[22],"called":[23],"molecular":[24,86],"docking":[25,87,103,135,205],"approaches.":[26],"To":[27,132,142],"evaluate":[28],"against":[30],"each":[31],"other,":[32],"scoring":[33,41,114,240],"functions":[34,42,157,241],"are":[35],"required.":[36],"In":[37,61],"recent":[38],"years":[39],"knowledge-based":[40,80],"have":[43],"been":[44,67],"evolved.":[45],"They":[46],"exploit":[47],"vast":[49],"amount":[50],"experimentally":[52],"determined":[53],"structures":[54],"to":[55,150,170,175],"derive":[56],"statistical":[57],"atom":[58,119],"pair":[59,120],"potentials.":[60],"this":[62],"work,":[63],"focus":[65],"has":[66],"set":[68,223],"on":[69],"implementation":[71,110],"and":[72,78,100,187,227],"validation":[74],"fast":[77],"robust":[79],"objective":[81,156],"function":[82,115],"PMF04":[83,113],"into":[84],"program":[88,104,145,206],"PARADDOCKS":[89,94,195,235],"(Parallel":[90],"Docking":[91],"Suite)":[92],"[1].":[93],"a":[96,158,167,222],"flexible,":[97],"easily":[98],"extensible":[99],"open":[101],"source":[102],"developed":[105],"in":[106,230,243],"our":[107],"group.\r\n\r\nFor":[108],"we":[116],"extracted":[117],"potentials":[121],"from":[122,213],"publicly":[124],"available":[125,204,239],"potential":[126],"mean":[128],"force":[129],"(PMF)":[130],"[2].":[131],"avoid":[133],"unfavourable":[134],"conformations":[136],"additional":[137],"an":[138],"vdW-term":[139],"was":[140,199],"added.":[141],"make":[143],"more":[146],"easy":[147],"for":[148,196],"developers":[149],"incorporate":[151],"own":[153],"or":[154],"adapted":[155],"Subgraph":[159],"Search":[160],"Description":[161],"(PSSD)":[162],"implemented.":[164],"It":[165],"line":[168],"notation":[169],"describe":[171],"subgraph":[172],"patterns":[173],"similar":[174],"SMARTS.":[176],"primary":[178],"difference":[179],"lack":[182],"implicit":[184,188],"hydrogen":[185],"treatment":[186],"bonds.\r\n\r\nIn":[189],"following,":[191],"performance":[193],"virtual":[197],"screening":[198],"compared":[200],"with":[201],"commercially":[203],"GOLD.":[207,244],"Therefore":[208],"13":[209],"targets":[210],"were":[211],"selected":[212],"directory":[215],"useful":[217],"decoys":[218],"(DUD)":[219],"which":[220],"contains":[221],"unbiased":[225],"actives":[226],"decoys.":[228],"Especially":[229],"terms":[231],"early":[233],"enrichment":[234],"outperforms":[236],"three":[238],"implemented":[242]},"counts_by_year":[{"year":2022,"cited_by_count":1}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}