{"id":"https://openalex.org/W4399759145","doi":"https://doi.org/10.1021/acs.jcim.6c00423","title":"Efficient and Precise Force Field Optimization for Biomolecules Using DPA-3","display_name":"Efficient and Precise Force Field Optimization for Biomolecules Using DPA-3","publication_year":2026,"publication_date":"2026-05-28","ids":{"openalex":"https://openalex.org/W4399759145","doi":"https://doi.org/10.1021/acs.jcim.6c00423","pmid":"https://pubmed.ncbi.nlm.nih.gov/42207492"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.6c00423","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6c00423","pdf_url":null,"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":null,"license_id":null,"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":["arxiv","crossref","datacite","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2406.09817","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000144720","display_name":"Junhan Chang","orcid":"https://orcid.org/0000-0003-3195-0773"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]},{"id":"https://openalex.org/I4210144013","display_name":"SP Technology (South Korea)","ror":"https://ror.org/051mxsx19","country_code":"KR","type":"company","lineage":["https://openalex.org/I4210144013"]}],"countries":["CN","KR"],"is_corresponding":false,"raw_author_name":"Junhan Chang","raw_affiliation_strings":["College of Chemistry and Molecular Engineering","DP Technology","Peking University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Chemistry and Molecular Engineering","institution_ids":[]},{"raw_affiliation_string":"DP Technology","institution_ids":["https://openalex.org/I4210144013"]},{"raw_affiliation_string":"Peking University","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100461295","display_name":"Duo Zhang","orcid":"https://orcid.org/0000-0001-9591-2659"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhe Xu","raw_affiliation_strings":["College of Chemistry and Molecular Engineering","Peking University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Chemistry and Molecular Engineering","institution_ids":[]},{"raw_affiliation_string":"Peking University","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064548885","display_name":"Yuqing Deng","orcid":null},"institutions":[{"id":"https://openalex.org/I2799847335","display_name":"Art Institute of Portland","ror":"https://ror.org/01cb0jg64","country_code":"US","type":"education","lineage":["https://openalex.org/I2799847335","https://openalex.org/I2799969541"]},{"id":"https://openalex.org/I4210144013","display_name":"SP Technology (South Korea)","ror":"https://ror.org/051mxsx19","country_code":"KR","type":"company","lineage":["https://openalex.org/I4210144013"]}],"countries":["KR","US"],"is_corresponding":false,"raw_author_name":"Duo Zhang","raw_affiliation_strings":["AI for Science Institute","DP Technology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"AI for Science Institute","institution_ids":["https://openalex.org/I2799847335"]},{"raw_affiliation_string":"DP Technology","institution_ids":["https://openalex.org/I4210144013"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076628024","display_name":"Hongrui Lin","orcid":"https://orcid.org/0000-0003-1053-7584"},"institutions":[{"id":"https://openalex.org/I4210144013","display_name":"SP Technology (South Korea)","ror":"https://ror.org/051mxsx19","country_code":"KR","type":"company","lineage":["https://openalex.org/I4210144013"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Hongrui Lin","raw_affiliation_strings":["DP Technology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"DP Technology","institution_ids":["https://openalex.org/I4210144013"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080579774","display_name":"Zhirong Liu","orcid":"https://orcid.org/0000-0001-5070-8048"},"institutions":[{"id":"https://openalex.org/I4210144013","display_name":"SP Technology (South Korea)","ror":"https://ror.org/051mxsx19","country_code":"KR","type":"company","lineage":["https://openalex.org/I4210144013"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Weijie Sun","raw_affiliation_strings":["DP Technology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"DP Technology","institution_ids":["https://openalex.org/I4210144013"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100689117","display_name":"Linfeng Zhang","orcid":"https://orcid.org/0000-0002-8470-5846"},"institutions":[{"id":"https://openalex.org/I2799847335","display_name":"Art Institute of Portland","ror":"https://ror.org/01cb0jg64","country_code":"US","type":"education","lineage":["https://openalex.org/I2799847335","https://openalex.org/I2799969541"]},{"id":"https://openalex.org/I4210144013","display_name":"SP Technology (South Korea)","ror":"https://ror.org/051mxsx19","country_code":"KR","type":"company","lineage":["https://openalex.org/I4210144013"]}],"countries":["KR","US"],"is_corresponding":false,"raw_author_name":"Linfeng Zhang","raw_affiliation_strings":["AI for Science Institute","DP Technology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"AI for Science Institute","institution_ids":["https://openalex.org/I2799847335"]},{"raw_affiliation_string":"DP Technology","institution_ids":["https://openalex.org/I4210144013"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102217501","display_name":"Hang Zheng","orcid":null},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zhirong Liu","raw_affiliation_strings":["College of Chemistry and Molecular Engineering","Peking University"],"raw_orcid":"https://orcid.org/0000-0001-5070-8048","affiliations":[{"raw_affiliation_string":"College of Chemistry and Molecular Engineering","institution_ids":[]},{"raw_affiliation_string":"Peking University","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100410987","display_name":"Xinyan Wang","orcid":"https://orcid.org/0009-0005-0278-0287"},"institutions":[{"id":"https://openalex.org/I4210144013","display_name":"SP Technology (South Korea)","ror":"https://ror.org/051mxsx19","country_code":"KR","type":"company","lineage":["https://openalex.org/I4210144013"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"Hang Zheng","raw_affiliation_strings":["DP Technology"],"raw_orcid":"https://orcid.org/0000-0002-2825-0576","affiliations":[{"raw_affiliation_string":"DP Technology","institution_ids":["https://openalex.org/I4210144013"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100410987","display_name":"Xinyan Wang","orcid":"https://orcid.org/0009-0005-0278-0287"},"institutions":[{"id":"https://openalex.org/I4210144013","display_name":"SP Technology (South Korea)","ror":"https://ror.org/051mxsx19","country_code":"KR","type":"company","lineage":["https://openalex.org/I4210144013"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"Xinyan Wang","raw_affiliation_strings":["DP Technology"],"raw_orcid":"https://orcid.org/0000-0002-3690-2335","affiliations":[{"raw_affiliation_string":"DP Technology","institution_ids":["https://openalex.org/I4210144013"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5100410987","https://openalex.org/A5102217501"],"corresponding_institution_ids":["https://openalex.org/I20231570","https://openalex.org/I4210144013"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.00390952,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"66","issue":"11","first_page":"6418","last_page":"6428"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10923","display_name":"Force Microscopy Techniques and Applications","score":0.9549999833106995,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10923","display_name":"Force Microscopy Techniques and Applications","score":0.9549999833106995,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T13539","display_name":"thermodynamics and calorimetric analyses","score":0.9204000234603882,"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/biomolecule","display_name":"Biomolecule","score":0.7056370973587036},{"id":"https://openalex.org/keywords/force-field","display_name":"Force field (fiction)","score":0.5912953019142151},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.5526151657104492},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.42403462529182434},{"id":"https://openalex.org/keywords/nanotechnology","display_name":"Nanotechnology","score":0.3861178755760193},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.32299649715423584},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.18170037865638733},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.09724670648574829}],"concepts":[{"id":"https://openalex.org/C49853544","wikidata":"https://www.wikidata.org/wiki/Q206229","display_name":"Biomolecule","level":2,"score":0.7056370973587036},{"id":"https://openalex.org/C10803110","wikidata":"https://www.wikidata.org/wiki/Q1341441","display_name":"Force field (fiction)","level":2,"score":0.5912953019142151},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.5526151657104492},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.42403462529182434},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.3861178755760193},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.32299649715423584},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.18170037865638733},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.09724670648574829},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D011789","descriptor_name":"Quantum Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011789","descriptor_name":"Quantum Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D047428","descriptor_name":"Protein Kinase Inhibitors","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D047428","descriptor_name":"Protein Kinase Inhibitors","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D047428","descriptor_name":"Protein Kinase Inhibitors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D047428","descriptor_name":"Protein Kinase Inhibitors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D053634","descriptor_name":"TYK2 Kinase","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":false},{"descriptor_ui":"D053634","descriptor_name":"TYK2 Kinase","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":false},{"descriptor_ui":"D053634","descriptor_name":"TYK2 Kinase","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D053634","descriptor_name":"TYK2 Kinase","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D053634","descriptor_name":"TYK2 Kinase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D053634","descriptor_name":"TYK2 Kinase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D054562","descriptor_name":"Protein Tyrosine Phosphatase, Non-Receptor Type 1","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":false},{"descriptor_ui":"D054562","descriptor_name":"Protein Tyrosine Phosphatase, Non-Receptor Type 1","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":false},{"descriptor_ui":"D054562","descriptor_name":"Protein Tyrosine Phosphatase, Non-Receptor Type 1","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D054562","descriptor_name":"Protein Tyrosine Phosphatase, Non-Receptor Type 1","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D054562","descriptor_name":"Protein Tyrosine Phosphatase, Non-Receptor Type 1","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D054562","descriptor_name":"Protein Tyrosine Phosphatase, Non-Receptor Type 1","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":true}],"locations_count":4,"locations":[{"id":"doi:10.1021/acs.jcim.6c00423","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6c00423","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:42207492","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42207492","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:arXiv.org:2406.09817","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2406.09817","pdf_url":"https://arxiv.org/pdf/2406.09817","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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":"","raw_type":"text"},{"id":"doi:10.48550/arxiv.2406.09817","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2406.09817","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2406.09817","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2406.09817","pdf_url":"https://arxiv.org/pdf/2406.09817","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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":"","raw_type":"text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5999728192","display_name":null,"funder_award_id":"22473003","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4399759145.pdf","grobid_xml":"https://content.openalex.org/works/W4399759145.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2367089784","https://openalex.org/W4281383848","https://openalex.org/W2344707987","https://openalex.org/W3021795417","https://openalex.org/W3182059148","https://openalex.org/W2914491564","https://openalex.org/W2028396431","https://openalex.org/W4386497600","https://openalex.org/W1998848630","https://openalex.org/W2073308043"],"abstract_inverted_index":{"Molecular":[0],"simulations":[1],"are":[2],"essential":[3],"tools":[4,132],"in":[5,28],"computational":[6,50,78,135],"chemistry,":[7],"enabling":[8],"the":[9,39,48,107,118,134],"prediction":[10],"and":[11,16,33,47,67,110,113,131],"understanding":[12],"of":[13,19,42,52,120],"molecular":[14],"interactions":[15],"thermodynamic":[17],"properties":[18],"biomolecules.":[20],"However,":[21],"traditional":[22],"force":[23,72],"fields":[24],"face":[25],"significant":[26],"challenges":[27],"accurately":[29],"representing":[30],"novel":[31],"molecules":[32],"complex":[34],"chemical":[35,97],"environments":[36],"due":[37],"to":[38,70,95,106],"labor-intensive":[40],"process":[41,105],"manually":[43],"setting":[44],"optimization":[45],"parameters":[46,74],"high":[49],"cost":[51],"quantum":[53],"mechanical":[54],"calculations.":[55],"To":[56],"overcome":[57],"these":[58],"difficulties,":[59],"we":[60],"fine-tuned":[61,84],"a":[62,88],"high-accuracy":[63],"DPA-3":[64,85],"pretrained":[65],"model":[66,86],"applied":[68,103],"it":[69],"optimize":[71],"field":[73],"on-the-fly,":[75],"significantly":[76],"reducing":[77],"costs.":[79],"Our":[80],"method":[81],"combines":[82],"this":[83,104],"with":[87],"node-embedding-based":[89],"similarity":[90],"metric,":[91],"allowing":[92],"seamless":[93],"augmentation":[94],"new":[96],"species":[98],"without":[99],"manual":[100],"intervention.":[101],"We":[102],"TYK2":[108],"inhibitor":[109],"PTP1B":[111],"systems":[112],"demonstrated":[114],"its":[115],"effectiveness":[116],"through":[117],"improvement":[119],"free":[121],"energy":[122],"perturbation":[123],"calculation":[124],"results.":[125],"This":[126],"advancement":[127],"contributes":[128],"valuable":[129],"insights":[130],"for":[133],"chemistry":[136],"community.":[137]},"counts_by_year":[],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2024-06-18T00:00:00"}
