{"id":"https://openalex.org/W108835927","doi":"https://doi.org/10.1186/1758-2946-5-s1-p14","title":"Force-field-based minimizations of protein-ligand complexes in the blink of an eye","display_name":"Force-field-based minimizations of protein-ligand complexes in the blink of an eye","publication_year":2013,"publication_date":"2013-03-01","ids":{"openalex":"https://openalex.org/W108835927","doi":"https://doi.org/10.1186/1758-2946-5-s1-p14","mag":"108835927"},"language":"en","primary_location":{"id":"doi:10.1186/1758-2946-5-s1-p14","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-5-s1-p14","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-5-S1-P14","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/10.1186/1758-2946-5-S1-P14","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5022612210","display_name":"Lennart Heinzerling","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"]},{"id":"https://openalex.org/I70451448","display_name":"HAW Hamburg","ror":"https://ror.org/00fkqwx76","country_code":"DE","type":"education","lineage":["https://openalex.org/I70451448"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Lennart Heinzerling","raw_affiliation_strings":["Center for Bioinformatics, University of Hamburg, Hamburg, Germany","Center for Bioinformatics, University of Hamburg Hamburg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics, University of Hamburg, Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]},{"raw_affiliation_string":"Center for Bioinformatics, University of Hamburg Hamburg, Germany","institution_ids":["https://openalex.org/I159176309","https://openalex.org/I70451448"]}]},{"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"]},{"id":"https://openalex.org/I70451448","display_name":"HAW Hamburg","ror":"https://ror.org/00fkqwx76","country_code":"DE","type":"education","lineage":["https://openalex.org/I70451448"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Matthias Rarey","raw_affiliation_strings":["Center for Bioinformatics, University of Hamburg, Hamburg, Germany","Center for Bioinformatics, University of Hamburg Hamburg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics, University of Hamburg, Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]},{"raw_affiliation_string":"Center for Bioinformatics, University of Hamburg Hamburg, Germany","institution_ids":["https://openalex.org/I159176309","https://openalex.org/I70451448"]}]}],"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":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.00811333,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"5","issue":"S1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9998000264167786,"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":0.9998000264167786,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9995999932289124,"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/T13326","display_name":"Biochemical and Structural Characterization","score":0.9952999949455261,"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":0.6067025661468506},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.5572319626808167},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.4670511782169342},{"id":"https://openalex.org/keywords/force-field","display_name":"Force field (fiction)","score":0.45950645208358765},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.315541535615921},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.2640589475631714},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.08256268501281738},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.08247122168540955},{"id":"https://openalex.org/keywords/internal-medicine","display_name":"Internal medicine","score":0.06843173503875732}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6067025661468506},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.5572319626808167},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.4670511782169342},{"id":"https://openalex.org/C10803110","wikidata":"https://www.wikidata.org/wiki/Q1341441","display_name":"Force field (fiction)","level":2,"score":0.45950645208358765},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.315541535615921},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.2640589475631714},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.08256268501281738},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.08247122168540955},{"id":"https://openalex.org/C126322002","wikidata":"https://www.wikidata.org/wiki/Q11180","display_name":"Internal medicine","level":1,"score":0.06843173503875732},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1186/1758-2946-5-s1-p14","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-5-s1-p14","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-5-S1-P14","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:europepmc.org:2605465","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3606184","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:10.1186/1758-2946-5-s1-p14","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-5-s1-p14","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-5-S1-P14","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/W108835927.pdf","grobid_xml":"https://content.openalex.org/works/W108835927.grobid-xml"},"referenced_works_count":2,"referenced_works":["https://openalex.org/W1982441109","https://openalex.org/W2121123192"],"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/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2350741829","https://openalex.org/W2130043461","https://openalex.org/W2530322880"],"abstract_inverted_index":{"Basing":[0],"protein-ligand":[1,82,187,217],"optimizations":[2,106],"on":[3,104,179,225],"molecular":[4],"mechanics":[5],"force":[6],"fields":[7],"yields":[8],"high":[9],"accuracy":[10],"at":[11,77],"the":[12,27,64,78,85,120,129,170,180,185,192,197,202,208],"cost":[13],"of":[14,30,56,81,87,97,201,206],"speed.":[15],"We":[16],"address":[17],"this":[18,138],"dilemma":[19],"by":[20,25,132,173],"circumventing":[21],"unnecessary":[22],"calculations":[23],"and":[24,44,146,159,167],"harvesting":[26],"computational":[28,37],"power":[29],"graphics":[31],"processor":[32],"units":[33],"(GPUs).":[34],"This":[35,70,92],"novel":[36],"architecture":[38],"is":[39],"well":[40],"suited":[41],"for":[42,215],"parallelizing":[43],"massively":[45],"speeding":[46],"up":[47],"force-field-based":[48],"minimization":[49],"procedures.":[50],"Our":[51],"endeavor":[52],"encompasses":[53],"fundamental":[54],"adaptions":[55],"formerly":[57],"CPU-based":[58],"methods":[59],"in":[60,72,84,119,220],"order":[61],"to":[62,127,156],"take":[63],"GPU-specific":[65],"programming":[66],"paradigms":[67],"into":[68],"account.":[69],"results":[71],"force-field":[73],"kernels":[74],"uniquely":[75],"targeted":[76],"efficient":[79],"optimization":[80,130,213],"complexes":[83],"context":[86],"a":[88,175,216],"mostly":[89],"GPU-based":[90],"procedure.":[91],"procedure":[93,131],"constitutes":[94],"an":[95,212],"improvement":[96],"our":[98],"recently":[99],"published":[100],"method[1]":[101],"which":[102],"focuses":[103],"complex":[105,218],"with":[107],"rigid":[108],"proteins.":[109],"The":[110],"new":[111],"version":[112],"presented":[113],"here":[114],"features":[115],"side":[116],"chain":[117],"flexibility":[118],"protein's":[121],"active":[122],"site.":[123],"Additionally,":[124],"it":[125],"allows":[126],"guide":[128],"considering":[133],"pharmacophoric-type":[134],"geometric":[135],"constraints.":[136],"In":[137,149,204],"way,":[139],"we":[140,189],"exploit":[141],"knowledge":[142],"about":[143],"binding":[144],"modes":[145],"conformational":[147],"preferences.":[148],"detail,":[150],"preferred":[151],"dihedral":[152],"angles":[153],"are":[154,165],"annotated":[155],"rotatable":[157],"bonds":[158],"selected":[160],"key":[161],"hydrogen":[162],"bond":[163],"interactions":[164],"marked":[166],"conserved.\r\n\r\nWe":[168],"demonstrate":[169],"procedure's":[171],"potential":[172],"performing":[174],"large-scale":[176],"docking":[177],"run":[178,214],"Astex-non-native":[181],"set[2].":[182],"By":[183],"optimizing":[184],"resulting":[186],"complexes,":[188],"significantly":[190],"shift":[191],"more":[193],"promising":[194],"conformations":[195],"towards":[196],"crystal":[198],"structure":[199],"geometry":[200],"complex.":[203],"spite":[205],"using":[207],"full":[209],"point-to-point":[210],"potential,":[211],"finishes":[219],"less":[221],"than":[222],"500":[223],"ms":[224],"average.":[226]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}