{"id":"https://openalex.org/W1997777695","doi":"https://doi.org/10.1186/1758-2946-3-s1-p13","title":"Hydrogen placement in protein-ligand complexes under consideration of tautomerism","display_name":"Hydrogen placement in protein-ligand complexes under consideration of tautomerism","publication_year":2011,"publication_date":"2011-04-19","ids":{"openalex":"https://openalex.org/W1997777695","doi":"https://doi.org/10.1186/1758-2946-3-s1-p13","mag":"1997777695"},"language":"en","primary_location":{"id":"doi:10.1186/1758-2946-3-s1-p13","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-3-s1-p13","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-3-S1-P13","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/10.1186/1758-2946-3-S1-P13","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5086310415","display_name":"Stefan Bietz","orcid":null},"institutions":[{"id":"https://openalex.org/I159176309","display_name":"Universit\u00e4t Hamburg","ror":"https://ror.org/00g30e956","country_code":"DE","type":"education","lineage":["https://openalex.org/I159176309"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"S Bietz","raw_affiliation_strings":["ZBH \u2013 Center for Bioinformatics, University of Hamburg, Bundesstr. 43, 20146, Hamburg, Germany","ZBH Center for Bioinformatics, University of Hamburg, Hamburg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ZBH \u2013 Center for Bioinformatics, University of Hamburg, Bundesstr. 43, 20146, Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]},{"raw_affiliation_string":"ZBH Center for Bioinformatics, University of Hamburg, Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075399884","display_name":"Sascha Urbaczek","orcid":null},"institutions":[{"id":"https://openalex.org/I159176309","display_name":"Universit\u00e4t Hamburg","ror":"https://ror.org/00g30e956","country_code":"DE","type":"education","lineage":["https://openalex.org/I159176309"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"S Urbaczek","raw_affiliation_strings":["ZBH \u2013 Center for Bioinformatics, University of Hamburg, Bundesstr. 43, 20146, Hamburg, Germany","ZBH Center for Bioinformatics, University of Hamburg, Hamburg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ZBH \u2013 Center for Bioinformatics, University of Hamburg, Bundesstr. 43, 20146, Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]},{"raw_affiliation_string":"ZBH Center for Bioinformatics, University of Hamburg, Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083205378","display_name":"Matthias Rarey","orcid":"https://orcid.org/0000-0002-9553-6531"},"institutions":[{"id":"https://openalex.org/I159176309","display_name":"Universit\u00e4t Hamburg","ror":"https://ror.org/00g30e956","country_code":"DE","type":"education","lineage":["https://openalex.org/I159176309"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"M Rarey","raw_affiliation_strings":["ZBH \u2013 Center for Bioinformatics, University of Hamburg, Bundesstr. 43, 20146, Hamburg, Germany","ZBH Center for Bioinformatics, University of Hamburg, Hamburg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ZBH \u2013 Center for Bioinformatics, University of Hamburg, Bundesstr. 43, 20146, Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]},{"raw_affiliation_string":"ZBH Center for Bioinformatics, University of Hamburg, Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":0.3261,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.58948448,"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":0.9994999766349792,"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":0.9994999766349792,"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/T10798","display_name":"Crystallography and molecular interactions","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","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/tautomer","display_name":"Tautomer","score":0.9923083782196045},{"id":"https://openalex.org/keywords/protonation","display_name":"Protonation","score":0.7082287073135376},{"id":"https://openalex.org/keywords/hydrogen-bond","display_name":"Hydrogen bond","score":0.622768759727478},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.594556987285614},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.552716076374054},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.5292971134185791},{"id":"https://openalex.org/keywords/hydrogen","display_name":"Hydrogen","score":0.4629572033882141},{"id":"https://openalex.org/keywords/stability","display_name":"Stability (learning theory)","score":0.41300010681152344},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.29998883605003357},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.24879184365272522},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.1642170250415802},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.10111838579177856},{"id":"https://openalex.org/keywords/organic-chemistry","display_name":"Organic chemistry","score":0.08344659209251404}],"concepts":[{"id":"https://openalex.org/C111233374","wikidata":"https://www.wikidata.org/wiki/Q334640","display_name":"Tautomer","level":2,"score":0.9923083782196045},{"id":"https://openalex.org/C30095370","wikidata":"https://www.wikidata.org/wiki/Q899488","display_name":"Protonation","level":3,"score":0.7082287073135376},{"id":"https://openalex.org/C112887158","wikidata":"https://www.wikidata.org/wiki/Q169324","display_name":"Hydrogen bond","level":3,"score":0.622768759727478},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.594556987285614},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.552716076374054},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.5292971134185791},{"id":"https://openalex.org/C512968161","wikidata":"https://www.wikidata.org/wiki/Q556","display_name":"Hydrogen","level":2,"score":0.4629572033882141},{"id":"https://openalex.org/C112972136","wikidata":"https://www.wikidata.org/wiki/Q7595718","display_name":"Stability (learning theory)","level":2,"score":0.41300010681152344},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.29998883605003357},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.24879184365272522},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.1642170250415802},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.10111838579177856},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.08344659209251404},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0},{"id":"https://openalex.org/C145148216","wikidata":"https://www.wikidata.org/wiki/Q36496","display_name":"Ion","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/1758-2946-3-s1-p13","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-3-s1-p13","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-3-S1-P13","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:a7df7c07444f464a8107f924cc4a5b84","is_oa":true,"landing_page_url":"https://doaj.org/article/a7df7c07444f464a8107f924cc4a5b84","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 3, Iss Suppl 1, p P13 (2011)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2091947","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3083567","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-p13","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-3-s1-p13","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-3-S1-P13","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":[{"score":0.7699999809265137,"id":"https://metadata.un.org/sdg/16","display_name":"Peace, Justice and strong institutions"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1997777695.pdf","grobid_xml":"https://content.openalex.org/works/W1997777695.grobid-xml"},"referenced_works_count":3,"referenced_works":["https://openalex.org/W2102376488","https://openalex.org/W2123325078","https://openalex.org/W2160907977"],"related_works":["https://openalex.org/W2105466274","https://openalex.org/W2010636594","https://openalex.org/W2914268038","https://openalex.org/W4283711622","https://openalex.org/W2000027971","https://openalex.org/W2091591194","https://openalex.org/W2049273629","https://openalex.org/W1993849124","https://openalex.org/W2061414747","https://openalex.org/W2417721574"],"abstract_inverted_index":{"Protein-ligand":[0],"complexes":[1,159],"are":[2,91,186],"often":[3],"consulted":[4],"for":[5,94,109,151,224],"the":[6,18,24,45,63,95,101,104,113,122,134,152,165,184,195,208,242],"understanding":[7],"of":[8,13,20,26,47,65,78,89,103,115,121,137,154,164,172,183,197,220,251],"binding":[9],"modes":[10],"and":[11,75,81,97,119,124,133,139,188],"mechanisms":[12],"action":[14],"as":[15,17,51,70,72],"well":[16,71],"development":[19],"novel":[21],"drugs.":[22],"Unfortunately":[23],"resolution":[25],"most":[27,85,105],"x-ray":[28],"structures":[29],"is":[30,59,192,205],"too":[31],"low":[32],"to":[33,61,130,169,240],"resolve":[34],"hydrogen":[35,38,52,66,110,155,209,221],"atoms.":[36],"However,":[37],"positions":[39,156],"play":[40],"a":[41,144,148,176,198],"major":[42],"role":[43],"in":[44,84,100,157,167,207,248,254],"analysis":[46],"important":[48,60],"interaction":[49,234],"types":[50],"bonding":[53],"or":[54],"metal":[55],"interactions.":[56],"Therefore,":[57],"it":[58],"predict":[62],"orientation":[64],"containing":[67],"rotatable":[68],"groups":[69],"sensible":[73],"protonation":[74,117,138],"tautomeric":[76,140,162,178],"states":[77,118],"both":[79],"protein":[80,96],"ligand.":[82],"While":[83],"cases":[86],"these":[87],"degrees":[88,171],"freedom":[90],"still":[92],"manageable":[93],"therefore":[98],"incorporated":[99],"models":[102],"common":[106,170],"prediction":[107,153,219],"tools":[108],"placement":[111,210],"[1-3],":[112],"consideration":[114],"different":[116,180,233],"tautomers":[120,182,228,244],"ligand":[123,166,185,243],"their":[125,189],"relative":[126,190],"frequency":[127],"can,":[128],"due":[129],"chemical":[131],"multiplicity":[132],"physicochemical":[135],"complexity":[136],"equilibria,":[141],"easily":[142],"become":[143],"complicated":[145],"problem.\r\n\r\nWe":[146],"present":[147],"new":[149],"method":[150],"protein-ligand":[158,255],"that":[160,226,245],"considers":[161],"variability":[163],"addition":[168],"freedom.":[173],"Beginning":[174],"with":[175,229],"random":[177],"state,":[179],"reasonable":[181],"enumerated":[187],"stability":[191,231],"estimated":[193],"on":[194],"basis":[196],"heuristic":[199],"scoring":[200],"scheme.":[201],"This":[202],"tautomerism":[203,252],"model":[204],"integrated":[206],"application":[211],"Protoss":[212],"[3].\r\n\r\nOur":[213],"approach":[214],"permits":[215],"an":[216],"enhanced":[217],"automatic":[218],"positions,":[222],"especially":[223],"ligands":[225],"exhibit":[227],"similar":[230],"but":[232],"facilities.":[235],"Furthermore":[236],"we":[237],"were":[238,246],"able":[239],"reproduce":[241],"proposed":[247],"several":[249],"studies":[250],"preferences":[253],"complexes.":[256]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
