{"id":"https://openalex.org/W4412450265","doi":"https://doi.org/10.1007/s10822-025-00630-3","title":"Mechanistic insights into PROTAC-mediated degradation through an integrated framework of molecular dynamics, free energy landscapes, and quantum mechanics: A case study on kinase degraders","display_name":"Mechanistic insights into PROTAC-mediated degradation through an integrated framework of molecular dynamics, free energy landscapes, and quantum mechanics: A case study on kinase degraders","publication_year":2025,"publication_date":"2025-07-15","ids":{"openalex":"https://openalex.org/W4412450265","doi":"https://doi.org/10.1007/s10822-025-00630-3","pmid":"https://pubmed.ncbi.nlm.nih.gov/40665123"},"language":"en","primary_location":{"id":"doi:10.1007/s10822-025-00630-3","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-025-00630-3","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/A5033817222","display_name":"Ashis Nandy","orcid":"https://orcid.org/0000-0002-9296-2535"},"institutions":[{"id":"https://openalex.org/I4210137452","display_name":"Drug Discovery Laboratory (Norway)","ror":"https://ror.org/04nybae35","country_code":"NO","type":"company","lineage":["https://openalex.org/I4210137452"]}],"countries":["NO"],"is_corresponding":true,"raw_author_name":"Ashis Nandy","raw_affiliation_strings":["Integrated Drug Discovery, Aragen Lifesciences Ltd, Hyderabad, 500076, India"],"affiliations":[{"raw_affiliation_string":"Integrated Drug Discovery, Aragen Lifesciences Ltd, Hyderabad, 500076, India","institution_ids":["https://openalex.org/I4210137452"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5118996706","display_name":"Kiran Boppana","orcid":null},"institutions":[{"id":"https://openalex.org/I4210137452","display_name":"Drug Discovery Laboratory (Norway)","ror":"https://ror.org/04nybae35","country_code":"NO","type":"company","lineage":["https://openalex.org/I4210137452"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Kiran Boppana","raw_affiliation_strings":["Integrated Drug Discovery, Aragen Lifesciences Ltd, Hyderabad, 500076, India"],"affiliations":[{"raw_affiliation_string":"Integrated Drug Discovery, Aragen Lifesciences Ltd, Hyderabad, 500076, India","institution_ids":["https://openalex.org/I4210137452"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025163851","display_name":"Samiron Phukan","orcid":"https://orcid.org/0000-0002-5009-2340"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Samiron Phukan","raw_affiliation_strings":["Integrated Drug Discovery, Aragen Lifesciences Ltd, Hyderabad, 500076, India. samiron.phukan@aragen.com"],"affiliations":[{"raw_affiliation_string":"Integrated Drug Discovery, Aragen Lifesciences Ltd, Hyderabad, 500076, India. samiron.phukan@aragen.com","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5033817222"],"corresponding_institution_ids":["https://openalex.org/I4210137452"],"apc_list":{"value":2890,"currency":"EUR","value_usd":3690},"apc_paid":null,"fwci":1.7468,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.85320455,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":96},"biblio":{"volume":"39","issue":"1","first_page":"51","last_page":"51"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12534","display_name":"Protein Degradation and Inhibitors","score":1.0,"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/T12534","display_name":"Protein Degradation and Inhibitors","score":1.0,"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/T11041","display_name":"Ubiquitin and proteasome pathways","score":0.9944999814033508,"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/T12505","display_name":"Peptidase Inhibition and Analysis","score":0.9810000061988831,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/molecular-mechanics","display_name":"Molecular mechanics","score":0.5684148669242859},{"id":"https://openalex.org/keywords/degradation","display_name":"Degradation (telecommunications)","score":0.46215277910232544},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.4588056802749634},{"id":"https://openalex.org/keywords/quantum","display_name":"Quantum","score":0.4108518362045288},{"id":"https://openalex.org/keywords/chemical-physics","display_name":"Chemical physics","score":0.3567129373550415},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3332160711288452},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3174211084842682},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.31590536236763},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.23247584700584412},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.20265331864356995}],"concepts":[{"id":"https://openalex.org/C25057246","wikidata":"https://www.wikidata.org/wiki/Q1344441","display_name":"Molecular mechanics","level":3,"score":0.5684148669242859},{"id":"https://openalex.org/C2779679103","wikidata":"https://www.wikidata.org/wiki/Q5251805","display_name":"Degradation (telecommunications)","level":2,"score":0.46215277910232544},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.4588056802749634},{"id":"https://openalex.org/C84114770","wikidata":"https://www.wikidata.org/wiki/Q46344","display_name":"Quantum","level":2,"score":0.4108518362045288},{"id":"https://openalex.org/C159467904","wikidata":"https://www.wikidata.org/wiki/Q2001702","display_name":"Chemical physics","level":1,"score":0.3567129373550415},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3332160711288452},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3174211084842682},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.31590536236763},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.23247584700584412},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.20265331864356995},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000098222","descriptor_name":"Quantum Mechanics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098222","descriptor_name":"Quantum Mechanics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098222","descriptor_name":"Quantum Mechanics","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":"D006801","descriptor_name":"Humans","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":"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":"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":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D044767","descriptor_name":"Ubiquitin-Protein Ligases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D044767","descriptor_name":"Ubiquitin-Protein Ligases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D044767","descriptor_name":"Ubiquitin-Protein Ligases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D044767","descriptor_name":"Ubiquitin-Protein Ligases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D044767","descriptor_name":"Ubiquitin-Protein Ligases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D044767","descriptor_name":"Ubiquitin-Protein Ligases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D054875","descriptor_name":"Ubiquitination","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054875","descriptor_name":"Ubiquitination","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054875","descriptor_name":"Ubiquitination","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":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059748","descriptor_name":"Proteolysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059748","descriptor_name":"Proteolysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059748","descriptor_name":"Proteolysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1007/s10822-025-00630-3","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-025-00630-3","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:40665123","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40665123","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":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Affordable and clean energy","score":0.4099999964237213,"id":"https://metadata.un.org/sdg/7"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":48,"referenced_works":["https://openalex.org/W1970549136","https://openalex.org/W1985865458","https://openalex.org/W2023271753","https://openalex.org/W2037950631","https://openalex.org/W2043686550","https://openalex.org/W2050885698","https://openalex.org/W2063663126","https://openalex.org/W2143981217","https://openalex.org/W2171249995","https://openalex.org/W2597078857","https://openalex.org/W2616655501","https://openalex.org/W2788356134","https://openalex.org/W2883024539","https://openalex.org/W2901669535","https://openalex.org/W2909353434","https://openalex.org/W2912114516","https://openalex.org/W2913446986","https://openalex.org/W2914587883","https://openalex.org/W2917115789","https://openalex.org/W2972312130","https://openalex.org/W2981722541","https://openalex.org/W3016041115","https://openalex.org/W3049752974","https://openalex.org/W3081555626","https://openalex.org/W3088011183","https://openalex.org/W3088870471","https://openalex.org/W3130894852","https://openalex.org/W3150635270","https://openalex.org/W3174791560","https://openalex.org/W3194728321","https://openalex.org/W3198775252","https://openalex.org/W3211270181","https://openalex.org/W4205379795","https://openalex.org/W4210495952","https://openalex.org/W4294941551","https://openalex.org/W4303954706","https://openalex.org/W4316669608","https://openalex.org/W4361298287","https://openalex.org/W4362601635","https://openalex.org/W4365509516","https://openalex.org/W4376872367","https://openalex.org/W4381850174","https://openalex.org/W4384205999","https://openalex.org/W4389663655","https://openalex.org/W4391428485","https://openalex.org/W4393117203","https://openalex.org/W4398179753","https://openalex.org/W4401074349"],"related_works":["https://openalex.org/W2414729539","https://openalex.org/W4315498887","https://openalex.org/W2034563028","https://openalex.org/W2000096903","https://openalex.org/W2316398224","https://openalex.org/W1990241706","https://openalex.org/W1980551862","https://openalex.org/W4281654480","https://openalex.org/W4380998201","https://openalex.org/W3006970086"],"abstract_inverted_index":null,"counts_by_year":[{"year":2025,"cited_by_count":2}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}
