{"id":"https://openalex.org/W7128195516","doi":"https://doi.org/10.1021/acs.jcim.5c02852","title":"DFDD: A Cloud-Ready Tool for Distance-Guided Fully Dynamic Docking in Host\u2013Guest Complexation","display_name":"DFDD: A Cloud-Ready Tool for Distance-Guided Fully Dynamic Docking in Host\u2013Guest Complexation","publication_year":2026,"publication_date":"2026-02-07","ids":{"openalex":"https://openalex.org/W7128195516","doi":"https://doi.org/10.1021/acs.jcim.5c02852","pmid":"https://pubmed.ncbi.nlm.nih.gov/41653112"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c02852","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c02852","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.5c02852?ref=article_openPDF","source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.5c02852?ref=article_openPDF","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5006301028","display_name":"Kowit Hengphasatporn","orcid":"https://orcid.org/0000-0001-8501-3844"},"institutions":[{"id":"https://openalex.org/I146399215","display_name":"University of Tsukuba","ror":"https://ror.org/02956yf07","country_code":"JP","type":"education","lineage":["https://openalex.org/I146399215"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Kowit Hengphasatporn","raw_affiliation_strings":["Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan"],"raw_orcid":"https://orcid.org/0000-0001-8501-3844","affiliations":[{"raw_affiliation_string":"Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan","institution_ids":["https://openalex.org/I146399215"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5125285605","display_name":"Lian Duan","orcid":null},"institutions":[{"id":"https://openalex.org/I146399215","display_name":"University of Tsukuba","ror":"https://ror.org/02956yf07","country_code":"JP","type":"education","lineage":["https://openalex.org/I146399215"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Lian Duan","raw_affiliation_strings":["Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan"],"raw_orcid":"https://orcid.org/0009-0001-6713-587X","affiliations":[{"raw_affiliation_string":"Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan","institution_ids":["https://openalex.org/I146399215"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073404259","display_name":"Ryuhei HARADA","orcid":null},"institutions":[{"id":"https://openalex.org/I146399215","display_name":"University of Tsukuba","ror":"https://ror.org/02956yf07","country_code":"JP","type":"education","lineage":["https://openalex.org/I146399215"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Ryuhei Harada","raw_affiliation_strings":["Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan"],"raw_orcid":"https://orcid.org/0000-0001-7987-0540","affiliations":[{"raw_affiliation_string":"Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan","institution_ids":["https://openalex.org/I146399215"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5125327660","display_name":"Yasuteru Shigeta","orcid":null},"institutions":[{"id":"https://openalex.org/I146399215","display_name":"University of Tsukuba","ror":"https://ror.org/02956yf07","country_code":"JP","type":"education","lineage":["https://openalex.org/I146399215"]},{"id":"https://openalex.org/I158708052","display_name":"Chulalongkorn University","ror":"https://ror.org/028wp3y58","country_code":"TH","type":"education","lineage":["https://openalex.org/I158708052"]},{"id":"https://openalex.org/I4210138427","display_name":"Computational Physics (United States)","ror":"https://ror.org/03grsxg62","country_code":"US","type":"company","lineage":["https://openalex.org/I4210138427"]}],"countries":["JP","TH","US"],"is_corresponding":false,"raw_author_name":"Yasuteru Shigeta","raw_affiliation_strings":["Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan","Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Faculty of Science","Chulalongkorn University"],"raw_orcid":"https://orcid.org/0000-0002-3219-6007","affiliations":[{"raw_affiliation_string":"Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan","institution_ids":["https://openalex.org/I146399215"]},{"raw_affiliation_string":"Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Faculty of Science","institution_ids":["https://openalex.org/I4210138427"]},{"raw_affiliation_string":"Chulalongkorn University","institution_ids":["https://openalex.org/I158708052"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5006301028"],"corresponding_institution_ids":["https://openalex.org/I146399215"],"apc_list":null,"apc_paid":null,"fwci":33.6231,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.99514195,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"66","issue":"4","first_page":"1955","last_page":"1963"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.3296000063419342,"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":0.3296000063419342,"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/T11162","display_name":"Enzyme Structure and Function","score":0.18080000579357147,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.13940000534057617,"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/molecular-dynamics","display_name":"Molecular dynamics","score":0.7200999855995178},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.6219000220298767},{"id":"https://openalex.org/keywords/protonation","display_name":"Protonation","score":0.5091000199317932},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.4519999921321869},{"id":"https://openalex.org/keywords/system-dynamics","display_name":"System dynamics","score":0.3628999888896942},{"id":"https://openalex.org/keywords/qm/mm","display_name":"QM/MM","score":0.3407000005245209},{"id":"https://openalex.org/keywords/trajectory","display_name":"Trajectory","score":0.33570000529289246}],"concepts":[{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.7200999855995178},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.6219000220298767},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6054999828338623},{"id":"https://openalex.org/C30095370","wikidata":"https://www.wikidata.org/wiki/Q899488","display_name":"Protonation","level":3,"score":0.5091000199317932},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.4519999921321869},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4449000060558319},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.38839998841285706},{"id":"https://openalex.org/C77405623","wikidata":"https://www.wikidata.org/wiki/Q598451","display_name":"System dynamics","level":2,"score":0.3628999888896942},{"id":"https://openalex.org/C20803032","wikidata":"https://www.wikidata.org/wiki/Q207900","display_name":"QM/MM","level":3,"score":0.3407000005245209},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.33649998903274536},{"id":"https://openalex.org/C13662910","wikidata":"https://www.wikidata.org/wiki/Q193139","display_name":"Trajectory","level":2,"score":0.33570000529289246},{"id":"https://openalex.org/C131584629","wikidata":"https://www.wikidata.org/wiki/Q4308705","display_name":"Coupling (piping)","level":2,"score":0.32409998774528503},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.32249999046325684},{"id":"https://openalex.org/C140779682","wikidata":"https://www.wikidata.org/wiki/Q210868","display_name":"Sampling (signal processing)","level":3,"score":0.3010999858379364},{"id":"https://openalex.org/C2780799671","wikidata":"https://www.wikidata.org/wiki/Q17087362","display_name":"Transient (computer programming)","level":2,"score":0.29280000925064087},{"id":"https://openalex.org/C62752575","wikidata":"https://www.wikidata.org/wiki/Q6822487","display_name":"Metadynamics","level":3,"score":0.2797999978065491},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.25589999556541443},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.25369998812675476},{"id":"https://openalex.org/C2987691683","wikidata":"https://www.wikidata.org/wiki/Q210868","display_name":"Sampling time","level":2,"score":0.2508000135421753}],"mesh":[{"descriptor_ui":"D000067917","descriptor_name":"Cloud Computing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000067917","descriptor_name":"Cloud Computing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000067917","descriptor_name":"Cloud Computing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000067917","descriptor_name":"Cloud Computing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000067917","descriptor_name":"Cloud Computing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000067917","descriptor_name":"Cloud Computing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000067917","descriptor_name":"Cloud Computing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D047392","descriptor_name":"beta-Cyclodextrins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D047392","descriptor_name":"beta-Cyclodextrins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D047392","descriptor_name":"beta-Cyclodextrins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D047392","descriptor_name":"beta-Cyclodextrins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D047392","descriptor_name":"beta-Cyclodextrins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D047392","descriptor_name":"beta-Cyclodextrins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D047392","descriptor_name":"beta-Cyclodextrins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.5c02852","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c02852","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.5c02852?ref=article_openPDF","source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:41653112","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41653112","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 chemical information and modeling","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12933709","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12933709/","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.5c02852","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c02852","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.5c02852?ref=article_openPDF","source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.7190064787864685,"id":"https://metadata.un.org/sdg/10","display_name":"Reduced inequalities"}],"awards":[{"id":"https://openalex.org/G2108865049","display_name":null,"funder_award_id":"JPMJCR20B3","funder_id":"https://openalex.org/F4320320907","funder_display_name":"Japan Science and Technology Corporation"},{"id":"https://openalex.org/G294993162","display_name":null,"funder_award_id":"JPMJCR20B3","funder_id":"https://openalex.org/F4320338075","funder_display_name":"Core Research for Evolutional Science and Technology"},{"id":"https://openalex.org/G5895805911","display_name":"FMO/ML-Guided Drug Design: Accelerating Novel Inhibitor Development and Drug Discovery","funder_award_id":"24K20888","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G6961433269","display_name":null,"funder_award_id":"21H05269","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G8718220378","display_name":null,"funder_award_id":"23H04879","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G942462350","display_name":null,"funder_award_id":"23H02427","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320320907","display_name":"Japan Science and Technology Corporation","ror":"https://ror.org/00097mb19"},{"id":"https://openalex.org/F4320323954","display_name":"University of Tsukuba","ror":"https://ror.org/02956yf07"},{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"},{"id":"https://openalex.org/F4320338075","display_name":"Core Research for Evolutional Science and Technology","ror":"https://ror.org/00097mb19"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7128195516.pdf","grobid_xml":"https://content.openalex.org/works/W7128195516.grobid-xml"},"referenced_works_count":56,"referenced_works":["https://openalex.org/W1968984443","https://openalex.org/W1995095833","https://openalex.org/W1996905877","https://openalex.org/W2003065881","https://openalex.org/W2015688756","https://openalex.org/W2016033647","https://openalex.org/W2024852705","https://openalex.org/W2032592607","https://openalex.org/W2039104539","https://openalex.org/W2064360650","https://openalex.org/W2088252867","https://openalex.org/W2124246500","https://openalex.org/W2129039800","https://openalex.org/W2147993766","https://openalex.org/W2152630148","https://openalex.org/W2160723824","https://openalex.org/W2164846849","https://openalex.org/W2170711116","https://openalex.org/W2332712348","https://openalex.org/W2419572089","https://openalex.org/W2540491215","https://openalex.org/W2560713311","https://openalex.org/W2766774911","https://openalex.org/W2888465361","https://openalex.org/W2901315612","https://openalex.org/W2920724574","https://openalex.org/W2945775080","https://openalex.org/W3006560560","https://openalex.org/W3035965352","https://openalex.org/W3037000485","https://openalex.org/W3125150422","https://openalex.org/W3144002674","https://openalex.org/W3198461437","https://openalex.org/W3203800312","https://openalex.org/W3215883361","https://openalex.org/W4212953809","https://openalex.org/W4220703112","https://openalex.org/W4229658977","https://openalex.org/W4282934376","https://openalex.org/W4295196986","https://openalex.org/W4307567162","https://openalex.org/W4313236875","https://openalex.org/W4387440676","https://openalex.org/W4388722415","https://openalex.org/W4391652187","https://openalex.org/W4399242417","https://openalex.org/W4399258311","https://openalex.org/W4399876839","https://openalex.org/W4401100562","https://openalex.org/W4401760437","https://openalex.org/W4407900788","https://openalex.org/W4408923677","https://openalex.org/W4409318725","https://openalex.org/W4411670136","https://openalex.org/W4416552657","https://openalex.org/W7116946064"],"related_works":[],"abstract_inverted_index":{"Fully":[0,34],"dynamic":[1],"sampling":[2],"of":[3,40,95,102],"host-guest":[4,89,147,160],"inclusion":[5,47,119],"remains":[6],"difficult":[7,26],"because":[8],"conventional":[9,12],"docking":[10],"and":[11,25,66,98,105,123,155],"molecular":[13,51],"dynamics":[14,52],"simulations":[15],"can":[16],"sample":[17],"inclusion,":[18],"but":[19],"crystal-like":[20],"binding":[21,107],"is":[22,84,166],"typically":[23],"stochastic":[24],"to":[27,45,143],"reproduce.":[28],"Here,":[29],"we":[30],"introduce":[31],"DFDD":[32,56,115,164],"(Distance-Guided":[33],"Dynamic":[35],"Docking),":[36],"a":[37,70,112,153],"cloud-ready":[38],"implementation":[39],"the":[41,88,100,128],"LB-PaCS-MD":[42],"framework":[43,165],"designed":[44],"capture":[46],"processes":[48],"via":[49],"unbiased":[50],"in":[53],"explicit":[54],"solvent.":[55],"automates":[57],"system":[58],"setup,":[59],"parameter":[60],"generation,":[61],"iterative":[62],"short-cycle":[63],"MD":[64],"sampling,":[65],"trajectory":[67],"analysis":[68],"within":[69,121],"single":[71],"workflow":[72],"that":[73],"runs":[74],"on":[75],"Google":[76],"Colab":[77],"without":[78],"any":[79],"installation.":[80],"Progress":[81],"toward":[82],"complexation":[83,161],"guided":[85],"only":[86],"by":[87],"center-of-mass":[90],"distance,":[91],"allowing":[92],"force-free":[93],"exploration":[94],"insertion":[96,129],"pathways":[97],"enabling":[99],"recovery":[101],"both":[103],"stable":[104],"transient":[106],"modes.":[108],"Using":[109],"\u03b2-cyclodextrin":[110],"as":[111],"representative":[113],"host,":[114],"reproduces":[116],"experimentally":[117],"observed":[118],"geometries":[120],"minutes":[122],"reveals":[124],"intermediate":[125],"states":[126,141],"along":[127],"route.":[130],"Optional":[131],"coupling":[132],"with":[133],"pKaNET-Cloud":[134],"enables":[135],"pH-aware,":[136],"stereochemically":[137],"consistent":[138],"ligand":[139],"protonation":[140],"prior":[142],"simulation,":[144],"supporting":[145],"robust":[146],"modeling.":[148],"This":[149],"Application":[150],"Note":[151],"provides":[152],"transparent":[154],"accessible":[156],"platform":[157],"for":[158],"efficient":[159],"studies.":[162],"The":[163],"publicly":[167],"available":[168],"at":[169],"https://github.com/nyelidl/DFDD.":[170]},"counts_by_year":[{"year":2026,"cited_by_count":4}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2026-02-08T00:00:00"}
