{"id":"https://openalex.org/W2084113057","doi":"https://doi.org/10.1007/s10822-012-9606-6","title":"Computation of relative binding free energy for an inhibitor and its analogs binding with Erk kinase using thermodynamic integration MD simulation","display_name":"Computation of relative binding free energy for an inhibitor and its analogs binding with Erk kinase using thermodynamic integration MD simulation","publication_year":2012,"publication_date":"2012-09-17","ids":{"openalex":"https://openalex.org/W2084113057","doi":"https://doi.org/10.1007/s10822-012-9606-6","mag":"2084113057","pmid":"https://pubmed.ncbi.nlm.nih.gov/22986633"},"language":"en","primary_location":{"id":"doi:10.1007/s10822-012-9606-6","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-012-9606-6","pdf_url":null,"source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032994318","display_name":"Kuan-Wei Wu","orcid":null},"institutions":[{"id":"https://openalex.org/I134161618","display_name":"National Taiwan Normal University","ror":"https://ror.org/059dkdx38","country_code":"TW","type":"education","lineage":["https://openalex.org/I134161618"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Kuan-Wei Wu","raw_affiliation_strings":["Department of Chemistry, National Taiwan Normal University, Taipei, Taiwan","Department of Chemistry , National Taiwan Normal University , Taipei, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, National Taiwan Normal University, Taipei, Taiwan","institution_ids":["https://openalex.org/I134161618"]},{"raw_affiliation_string":"Department of Chemistry , National Taiwan Normal University , Taipei, Taiwan","institution_ids":["https://openalex.org/I134161618"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052224443","display_name":"Po-Chin Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I134161618","display_name":"National Taiwan Normal University","ror":"https://ror.org/059dkdx38","country_code":"TW","type":"education","lineage":["https://openalex.org/I134161618"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Po-Chin Chen","raw_affiliation_strings":["Department of Chemistry, National Taiwan Normal University, 88, TingChow Road Section 4, Taipei, 116, Taiwan","Department of Chemistry, National Taiwan Normal University, 88, TingChow Road Section\u00a04, Taipei, 116, Taiwan","National Taiwan Normal University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, National Taiwan Normal University, 88, TingChow Road Section 4, Taipei, 116, Taiwan","institution_ids":["https://openalex.org/I134161618"]},{"raw_affiliation_string":"Department of Chemistry, National Taiwan Normal University, 88, TingChow Road Section\u00a04, Taipei, 116, Taiwan","institution_ids":["https://openalex.org/I134161618"]},{"raw_affiliation_string":"National Taiwan Normal University","institution_ids":["https://openalex.org/I134161618"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100384846","display_name":"Jun Wang","orcid":"https://orcid.org/0000-0003-0222-6380"},"institutions":[{"id":"https://openalex.org/I134161618","display_name":"National Taiwan Normal University","ror":"https://ror.org/059dkdx38","country_code":"TW","type":"education","lineage":["https://openalex.org/I134161618"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Jun Wang","raw_affiliation_strings":["Department of Chemistry, National Taiwan Normal University, 88, TingChow Road Section 4, Taipei, 116, Taiwan","Department of Chemistry, National Taiwan Normal University, 88, TingChow Road Section\u00a04, Taipei, 116, Taiwan","National Taiwan Normal University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, National Taiwan Normal University, 88, TingChow Road Section 4, Taipei, 116, Taiwan","institution_ids":["https://openalex.org/I134161618"]},{"raw_affiliation_string":"Department of Chemistry, National Taiwan Normal University, 88, TingChow Road Section\u00a04, Taipei, 116, Taiwan","institution_ids":["https://openalex.org/I134161618"]},{"raw_affiliation_string":"National Taiwan Normal University","institution_ids":["https://openalex.org/I134161618"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100355569","display_name":"Ying\u2010Chieh Sun","orcid":null},"institutions":[{"id":"https://openalex.org/I134161618","display_name":"National Taiwan Normal University","ror":"https://ror.org/059dkdx38","country_code":"TW","type":"education","lineage":["https://openalex.org/I134161618"]}],"countries":["TW"],"is_corresponding":true,"raw_author_name":"Ying-Chieh Sun","raw_affiliation_strings":["Department of Chemistry, National Taiwan Normal University, 88, TingChow Road Section 4, Taipei, 116, Taiwan","Department of Chemistry, National Taiwan Normal University, 88, TingChow Road Section\u00a04, Taipei, 116, Taiwan","Department of Chemistry , National Taiwan Normal University , Taipei, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, National Taiwan Normal University, 88, TingChow Road Section 4, Taipei, 116, Taiwan","institution_ids":["https://openalex.org/I134161618"]},{"raw_affiliation_string":"Department of Chemistry, National Taiwan Normal University, 88, TingChow Road Section\u00a04, Taipei, 116, Taiwan","institution_ids":["https://openalex.org/I134161618"]},{"raw_affiliation_string":"Department of Chemistry , National Taiwan Normal University , Taipei, Taiwan","institution_ids":["https://openalex.org/I134161618"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5100355569"],"corresponding_institution_ids":["https://openalex.org/I134161618"],"apc_list":{"value":4190,"currency":"USD","value_usd":4190},"apc_paid":null,"fwci":3.568,"has_fulltext":false,"cited_by_count":27,"citation_normalized_percentile":{"value":0.93144975,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"26","issue":"10","first_page":"1159","last_page":"1169"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9986000061035156,"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":0.9986000061035156,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9980000257492065,"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":0.9901000261306763,"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/chemistry","display_name":"Chemistry","score":0.6238362193107605},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.6217241287231445},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.6040180325508118},{"id":"https://openalex.org/keywords/benzene","display_name":"Benzene","score":0.5672885179519653},{"id":"https://openalex.org/keywords/hydrogen-bond","display_name":"Hydrogen bond","score":0.5584121346473694},{"id":"https://openalex.org/keywords/thermodynamic-integration","display_name":"Thermodynamic integration","score":0.5559082627296448},{"id":"https://openalex.org/keywords/binding-energy","display_name":"Binding energy","score":0.5273590683937073},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.5195724964141846},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.46081939339637756},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.4401249587535858},{"id":"https://openalex.org/keywords/thermodynamics","display_name":"Thermodynamics","score":0.3544045090675354},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.35432004928588867},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.25502556562423706},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.1923694908618927},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.15990620851516724},{"id":"https://openalex.org/keywords/atomic-physics","display_name":"Atomic physics","score":0.15526223182678223},{"id":"https://openalex.org/keywords/organic-chemistry","display_name":"Organic chemistry","score":0.1308659315109253},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.11712810397148132},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.09126794338226318},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.07658842206001282}],"concepts":[{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.6238362193107605},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.6217241287231445},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.6040180325508118},{"id":"https://openalex.org/C2777691172","wikidata":"https://www.wikidata.org/wiki/Q2270","display_name":"Benzene","level":2,"score":0.5672885179519653},{"id":"https://openalex.org/C112887158","wikidata":"https://www.wikidata.org/wiki/Q169324","display_name":"Hydrogen bond","level":3,"score":0.5584121346473694},{"id":"https://openalex.org/C141780669","wikidata":"https://www.wikidata.org/wiki/Q7783161","display_name":"Thermodynamic integration","level":3,"score":0.5559082627296448},{"id":"https://openalex.org/C93282013","wikidata":"https://www.wikidata.org/wiki/Q420754","display_name":"Binding energy","level":2,"score":0.5273590683937073},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.5195724964141846},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.46081939339637756},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.4401249587535858},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.3544045090675354},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.35432004928588867},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.25502556562423706},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.1923694908618927},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.15990620851516724},{"id":"https://openalex.org/C184779094","wikidata":"https://www.wikidata.org/wiki/Q26383","display_name":"Atomic physics","level":1,"score":0.15526223182678223},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.1308659315109253},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.11712810397148132},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.09126794338226318},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.07658842206001282}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","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":true},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"D047428","descriptor_name":"Protein Kinase Inhibitors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D048049","descriptor_name":"Extracellular Signal-Regulated MAP Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D048049","descriptor_name":"Extracellular Signal-Regulated MAP Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D048049","descriptor_name":"Extracellular Signal-Regulated MAP Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1007/s10822-012-9606-6","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-012-9606-6","pdf_url":null,"source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},{"id":"pmid:22986633","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22986633","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 computer-aided molecular design","raw_type":"Journal Article"},{"id":"pmh:oai:ir.qibebt.ac.cn:337004/1321","is_oa":false,"landing_page_url":"http://124.16.151.184:8080/handle/337004/1321","pdf_url":null,"source":{"id":"https://openalex.org/S4306400842","display_name":"Institutional knowledge base (Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I19820366","host_organization_name":"Chinese Academy of Sciences","host_organization_lineage":["https://openalex.org/I19820366"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Kuan-Wei Wu; Po-Chin Chen; Jun Wang; Ying-Chieh Sun .Computation of relative binding free energy for an inhibitor and its analogs binding with Erk kinase using thermodynamic integration MD simulation .J Comput Aided Mol Des.,2012,26(10):1159-69","raw_type":"\u671f\u520a\u8bba\u6587"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Affordable and clean energy","score":0.8600000143051147,"id":"https://metadata.un.org/sdg/7"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":50,"referenced_works":["https://openalex.org/W1587176568","https://openalex.org/W1971561764","https://openalex.org/W1978842016","https://openalex.org/W1980618423","https://openalex.org/W1981806668","https://openalex.org/W1989195611","https://openalex.org/W1992056212","https://openalex.org/W1997612995","https://openalex.org/W2001368885","https://openalex.org/W2004124673","https://openalex.org/W2010882262","https://openalex.org/W2015688756","https://openalex.org/W2020649868","https://openalex.org/W2024553805","https://openalex.org/W2025820706","https://openalex.org/W2025829414","https://openalex.org/W2028835439","https://openalex.org/W2028841370","https://openalex.org/W2031888811","https://openalex.org/W2035177313","https://openalex.org/W2039353947","https://openalex.org/W2043383571","https://openalex.org/W2043429268","https://openalex.org/W2050774715","https://openalex.org/W2060002448","https://openalex.org/W2063604977","https://openalex.org/W2068782086","https://openalex.org/W2070915333","https://openalex.org/W2077416963","https://openalex.org/W2077954341","https://openalex.org/W2082630624","https://openalex.org/W2084550263","https://openalex.org/W2090149270","https://openalex.org/W2092082882","https://openalex.org/W2099282863","https://openalex.org/W2113657050","https://openalex.org/W2123766716","https://openalex.org/W2128494768","https://openalex.org/W2130159206","https://openalex.org/W2136803839","https://openalex.org/W2138778824","https://openalex.org/W2151020862","https://openalex.org/W2155554859","https://openalex.org/W2169017143","https://openalex.org/W2311078281","https://openalex.org/W2319609862","https://openalex.org/W2323898978","https://openalex.org/W2614429920","https://openalex.org/W2752932982","https://openalex.org/W3191210297"],"related_works":["https://openalex.org/W3027016565","https://openalex.org/W123874623","https://openalex.org/W2380764344","https://openalex.org/W1912959589","https://openalex.org/W2028872807","https://openalex.org/W2048564905","https://openalex.org/W2023538917","https://openalex.org/W3105421503","https://openalex.org/W3175840220","https://openalex.org/W2108339230"],"abstract_inverted_index":null,"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":5}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}