{"id":"https://openalex.org/W2123325078","doi":"https://doi.org/10.1186/1758-2946-1-13","title":"Fast automated placement of polar hydrogen atoms in protein-ligand complexes","display_name":"Fast automated placement of polar hydrogen atoms in protein-ligand complexes","publication_year":2009,"publication_date":"2009-08-12","ids":{"openalex":"https://openalex.org/W2123325078","doi":"https://doi.org/10.1186/1758-2946-1-13","mag":"2123325078","pmid":"https://pubmed.ncbi.nlm.nih.gov/20298519"},"language":"en","primary_location":{"id":"doi:10.1186/1758-2946-1-13","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-1-13","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-1-13","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","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-1-13","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5051614433","display_name":"Tobias Lippert","orcid":null},"institutions":[{"id":"https://openalex.org/I4210136595","display_name":"Hamburg Institut (Germany)","ror":"https://ror.org/03t0n2419","country_code":"DE","type":"company","lineage":["https://openalex.org/I4210136595"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Tobias Lippert","raw_affiliation_strings":["Center for Bioinformatics, 20146 Hamburg, Germany. rarey@zbh.uni-hamburg.de","Center for Bioinformatics, Hamburg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics, 20146 Hamburg, Germany. rarey@zbh.uni-hamburg.de","institution_ids":["https://openalex.org/I4210136595"]},{"raw_affiliation_string":"Center for Bioinformatics, Hamburg, Germany","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083205378","display_name":"Matthias Rarey","orcid":"https://orcid.org/0000-0002-9553-6531"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Matthias Rarey","raw_affiliation_strings":["Center for Bioinformatics, 20146, Hamburg, Germany","Center for Bioinformatics, Hamburg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics, 20146, Hamburg, Germany","institution_ids":[]},{"raw_affiliation_string":"Center for Bioinformatics, Hamburg, Germany","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"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":0.9585,"has_fulltext":true,"cited_by_count":91,"citation_normalized_percentile":{"value":0.75054116,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"1","issue":"1","first_page":"13","last_page":"13"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.8151000142097473,"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":0.8151000142097473,"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/T11162","display_name":"Enzyme Structure and Function","score":0.09960000216960907,"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"}},{"id":"https://openalex.org/T10798","display_name":"Crystallography and molecular interactions","score":0.02199999988079071,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/hydrogen-bond","display_name":"Hydrogen bond","score":0.7724734544754028},{"id":"https://openalex.org/keywords/low-barrier-hydrogen-bond","display_name":"Low-barrier hydrogen bond","score":0.6681932210922241},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.5878980159759521},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.5300243496894836},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.499434232711792},{"id":"https://openalex.org/keywords/hydrogen","display_name":"Hydrogen","score":0.4862900674343109},{"id":"https://openalex.org/keywords/hydrogen-atom","display_name":"Hydrogen atom","score":0.4742297828197479},{"id":"https://openalex.org/keywords/amide","display_name":"Amide","score":0.46857690811157227},{"id":"https://openalex.org/keywords/tautomer","display_name":"Tautomer","score":0.46001267433166504},{"id":"https://openalex.org/keywords/spin-isomers-of-hydrogen","display_name":"Spin isomers of hydrogen","score":0.45935535430908203},{"id":"https://openalex.org/keywords/histidine","display_name":"Histidine","score":0.45179933309555054},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.42735517024993896},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.3641526401042938},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.277222216129303},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.20753106474876404},{"id":"https://openalex.org/keywords/group","display_name":"Group (periodic table)","score":0.17192989587783813},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.11930921673774719}],"concepts":[{"id":"https://openalex.org/C112887158","wikidata":"https://www.wikidata.org/wiki/Q169324","display_name":"Hydrogen bond","level":3,"score":0.7724734544754028},{"id":"https://openalex.org/C139286075","wikidata":"https://www.wikidata.org/wiki/Q909717","display_name":"Low-barrier hydrogen bond","level":4,"score":0.6681932210922241},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5878980159759521},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.5300243496894836},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.499434232711792},{"id":"https://openalex.org/C512968161","wikidata":"https://www.wikidata.org/wiki/Q556","display_name":"Hydrogen","level":2,"score":0.4862900674343109},{"id":"https://openalex.org/C2776640939","wikidata":"https://www.wikidata.org/wiki/Q6643508","display_name":"Hydrogen atom","level":3,"score":0.4742297828197479},{"id":"https://openalex.org/C2778439535","wikidata":"https://www.wikidata.org/wiki/Q188777","display_name":"Amide","level":2,"score":0.46857690811157227},{"id":"https://openalex.org/C111233374","wikidata":"https://www.wikidata.org/wiki/Q334640","display_name":"Tautomer","level":2,"score":0.46001267433166504},{"id":"https://openalex.org/C19449701","wikidata":"https://www.wikidata.org/wiki/Q385696","display_name":"Spin isomers of hydrogen","level":3,"score":0.45935535430908203},{"id":"https://openalex.org/C2778460671","wikidata":"https://www.wikidata.org/wiki/Q485277","display_name":"Histidine","level":3,"score":0.45179933309555054},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.42735517024993896},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.3641526401042938},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.277222216129303},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.20753106474876404},{"id":"https://openalex.org/C2781311116","wikidata":"https://www.wikidata.org/wiki/Q83306","display_name":"Group (periodic table)","level":2,"score":0.17192989587783813},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.11930921673774719},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"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/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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":4,"locations":[{"id":"doi:10.1186/1758-2946-1-13","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-1-13","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-1-13","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":"pmid:20298519","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20298519","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":"Journal of cheminformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:deebd07cf16b4467894896df6f97d7fa","is_oa":false,"landing_page_url":"https://doaj.org/article/deebd07cf16b4467894896df6f97d7fa","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 1, Iss 1, p 13 (2009)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3225823","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3225823","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"}],"best_oa_location":{"id":"doi:10.1186/1758-2946-1-13","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-1-13","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-1-13","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":[{"display_name":"Peace, Justice and strong institutions","id":"https://metadata.un.org/sdg/16","score":0.7699999809265137}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2123325078.pdf","grobid_xml":"https://content.openalex.org/works/W2123325078.grobid-xml"},"referenced_works_count":29,"referenced_works":["https://openalex.org/W284549920","https://openalex.org/W1500385977","https://openalex.org/W1557981632","https://openalex.org/W1656114533","https://openalex.org/W1965784613","https://openalex.org/W1983194490","https://openalex.org/W1998502755","https://openalex.org/W2005481380","https://openalex.org/W2010004274","https://openalex.org/W2015403140","https://openalex.org/W2034434306","https://openalex.org/W2043062020","https://openalex.org/W2056000901","https://openalex.org/W2059981265","https://openalex.org/W2060059149","https://openalex.org/W2071196096","https://openalex.org/W2083965528","https://openalex.org/W2092285329","https://openalex.org/W2102376488","https://openalex.org/W2111633834","https://openalex.org/W2114779636","https://openalex.org/W2115339329","https://openalex.org/W2130479394","https://openalex.org/W2142820798","https://openalex.org/W2147421370","https://openalex.org/W2149026172","https://openalex.org/W2151256267","https://openalex.org/W2160907977","https://openalex.org/W4301383974"],"related_works":["https://openalex.org/W2105466274","https://openalex.org/W2010636594","https://openalex.org/W4283711622","https://openalex.org/W2000027971","https://openalex.org/W2049273629","https://openalex.org/W3002554271","https://openalex.org/W2914268038","https://openalex.org/W2074891539","https://openalex.org/W2740116981","https://openalex.org/W4220994561"],"abstract_inverted_index":{"BACKGROUND:":[0],"Hydrogen":[1],"bonds":[2,48],"play":[3],"a":[4,16,66,90,102,135,146,204],"major":[5],"role":[6],"in":[7,39,89,110,145,165],"the":[8,24,34,76,79,85,96,139,223,226,246],"stabilization":[9],"of":[10,15,26,33,36,55,61,78,98,151,203,225,235,242,248],"protein-ligand":[11,148,172],"complexes.":[12],"The":[13,52,233],"ability":[14],"functional":[17,103],"group":[18,104],"to":[19,44,137,170,182,240,252],"form":[20],"them":[21],"depends":[22],"on":[23],"position":[25,77],"its":[27,70],"hydrogen":[28,37,47,56,67,80,99,142,152,227],"atoms.":[29],"An":[30],"accurate":[31],"knowledge":[32],"positions":[35,144,224],"atoms":[38,57,100,228],"proteins":[40],"is":[41,82,155,163,238],"therefore":[42],"important":[43],"correctly":[45],"identify":[46],"and":[49,92,112,114,193],"their":[50],"properties.":[51],"high":[53,198],"mobility":[54],"introduces":[58],"several":[59],"degrees":[60],"freedom:":[62],"Tautomeric":[63],"states,":[64,94],"where":[65,75,95],"atom":[68,81,143],"alters":[69],"binding":[71],"partner,":[72],"torsional":[73],"changes":[74],"rotated":[83],"around":[84],"last":[86],"heavy-atom":[87],"bond":[88,153],"residue,":[91],"protonation":[93],"number":[97],"at":[101],"may":[105],"change.":[106],"Also,":[107,178],"side-chain":[108],"flips":[109],"glutamine":[111],"asparagine":[113],"histidine":[115,194],"residues,":[116],"which":[117,162,222],"are":[118],"common":[119,184],"crystallographic":[120,185],"ambiguities":[121,186],"must":[122],"be":[123,129,253],"identified":[124],"before":[125],"structure-based":[126],"calculations":[127],"can":[128],"conducted.":[130],"RESULTS:":[131],"We":[132],"have":[133,229],"implemented":[134],"method":[136,180],"determine":[138],"most":[140],"probable":[141],"given":[147],"complex.":[149],"Optimality":[150],"geometries":[154],"determined":[156],"by":[157],"an":[158,175,218],"empirical":[159],"scoring":[160],"function":[161],"used":[164],"molecular":[166],"docking.":[167],"This":[168],"allows":[169,181],"evaluate":[171],"interactions":[173],"with":[174,245],"established":[176],"model.":[177],"our":[179,236],"resolve":[183],"such":[187],"as":[188,189],"flipped":[190],"amide":[191],"groups":[192],"residues.":[195],"To":[196],"ensure":[197],"speed,":[199],"we":[200],"make":[201],"use":[202],"dynamic":[205],"programming":[206],"approach.":[207],"CONCLUSION:":[208],"Our":[209],"results":[210,237],"were":[211],"checked":[212],"against":[213],"selected":[214],"high-resolution":[215],"structures":[216],"from":[217],"external":[219],"dataset,":[220],"for":[221,256],"been":[230],"validated":[231],"manually.":[232],"quality":[234],"comparable":[239],"that":[241],"other":[243],"programs,":[244],"advantage":[247],"being":[249],"fast":[250],"enough":[251],"applied":[254],"on-the-fly":[255],"interactive":[257],"usage":[258],"or":[259],"during":[260],"score":[261],"evaluation.":[262]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":14},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":14},{"year":2022,"cited_by_count":17},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":3},{"year":2014,"cited_by_count":5},{"year":2012,"cited_by_count":3}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}