{"id":"https://openalex.org/W4405436010","doi":"https://doi.org/10.1021/acs.jcim.4c01612","title":"Leveraging the Thermodynamics of Protein Conformations in Drug Discovery","display_name":"Leveraging the Thermodynamics of Protein Conformations in Drug Discovery","publication_year":2024,"publication_date":"2024-12-16","ids":{"openalex":"https://openalex.org/W4405436010","doi":"https://doi.org/10.1021/acs.jcim.4c01612","pmid":"https://pubmed.ncbi.nlm.nih.gov/39681511"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.4c01612","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01612","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":["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/A5039141057","display_name":"Bin W. Zhang","orcid":"https://orcid.org/0000-0003-3007-4900"},"institutions":[{"id":"https://openalex.org/I203455613","display_name":"Schrodinger (United States)","ror":"https://ror.org/05a3z6914","country_code":"US","type":"company","lineage":["https://openalex.org/I203455613"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Bin W. Zhang","raw_affiliation_strings":["Schr\u00f6dinger Inc., 1540 Broadway, 24th Floor, New York, New York 10036-4041, United States"],"raw_orcid":"https://orcid.org/0000-0003-3007-4900","affiliations":[{"raw_affiliation_string":"Schr\u00f6dinger Inc., 1540 Broadway, 24th Floor, New York, New York 10036-4041, United States","institution_ids":["https://openalex.org/I203455613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025402203","display_name":"Mikolai Fajer","orcid":"https://orcid.org/0000-0003-2116-3514"},"institutions":[{"id":"https://openalex.org/I203455613","display_name":"Schrodinger (United States)","ror":"https://ror.org/05a3z6914","country_code":"US","type":"company","lineage":["https://openalex.org/I203455613"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mikolai Fajer","raw_affiliation_strings":["Schr\u00f6dinger Inc., 1540 Broadway, 24th Floor, New York, New York 10036-4041, United States"],"raw_orcid":"https://orcid.org/0000-0003-2116-3514","affiliations":[{"raw_affiliation_string":"Schr\u00f6dinger Inc., 1540 Broadway, 24th Floor, New York, New York 10036-4041, United States","institution_ids":["https://openalex.org/I203455613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020861476","display_name":"Wei Chen","orcid":"https://orcid.org/0000-0003-2647-3888"},"institutions":[{"id":"https://openalex.org/I203455613","display_name":"Schrodinger (United States)","ror":"https://ror.org/05a3z6914","country_code":"US","type":"company","lineage":["https://openalex.org/I203455613"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wei Chen","raw_affiliation_strings":["Schr\u00f6dinger Inc., 1540 Broadway, 24th Floor, New York, New York 10036-4041, United States"],"raw_orcid":"https://orcid.org/0000-0003-2647-3888","affiliations":[{"raw_affiliation_string":"Schr\u00f6dinger Inc., 1540 Broadway, 24th Floor, New York, New York 10036-4041, United States","institution_ids":["https://openalex.org/I203455613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059258417","display_name":"Francesca Moraca","orcid":"https://orcid.org/0000-0003-0248-9834"},"institutions":[{"id":"https://openalex.org/I203455613","display_name":"Schrodinger (United States)","ror":"https://ror.org/05a3z6914","country_code":"US","type":"company","lineage":["https://openalex.org/I203455613"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Francesca Moraca","raw_affiliation_strings":["Schr\u00f6dinger Inc., 1540 Broadway, 24th Floor, New York, New York 10036-4041, United States"],"raw_orcid":"https://orcid.org/0000-0003-0248-9834","affiliations":[{"raw_affiliation_string":"Schr\u00f6dinger Inc., 1540 Broadway, 24th Floor, New York, New York 10036-4041, United States","institution_ids":["https://openalex.org/I203455613"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5073422740","display_name":"Lingle Wang","orcid":"https://orcid.org/0000-0002-8170-6798"},"institutions":[{"id":"https://openalex.org/I203455613","display_name":"Schrodinger (United States)","ror":"https://ror.org/05a3z6914","country_code":"US","type":"company","lineage":["https://openalex.org/I203455613"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Lingle Wang","raw_affiliation_strings":["Schr\u00f6dinger Inc., 1540 Broadway, 24th Floor, New York, New York 10036-4041, United States"],"raw_orcid":"https://orcid.org/0000-0002-8170-6798","affiliations":[{"raw_affiliation_string":"Schr\u00f6dinger Inc., 1540 Broadway, 24th Floor, New York, New York 10036-4041, United States","institution_ids":["https://openalex.org/I203455613"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5025402203","https://openalex.org/A5039141057","https://openalex.org/A5073422740"],"corresponding_institution_ids":["https://openalex.org/I203455613"],"apc_list":null,"apc_paid":null,"fwci":0.2152,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.5887673,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"65","issue":"1","first_page":"252","last_page":"264"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9980999827384949,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9977999925613403,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.7275779247283936},{"id":"https://openalex.org/keywords/ambiguity","display_name":"Ambiguity","score":0.6602654457092285},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.597796618938446},{"id":"https://openalex.org/keywords/conformational-ensembles","display_name":"Conformational ensembles","score":0.5004079341888428},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.47117215394973755},{"id":"https://openalex.org/keywords/drug-target","display_name":"Drug target","score":0.4329261779785156},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4305740296840668},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.41637319326400757},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.36441701650619507},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.32151907682418823},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2231004238128662},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.1711527407169342}],"concepts":[{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.7275779247283936},{"id":"https://openalex.org/C2780522230","wikidata":"https://www.wikidata.org/wiki/Q1140419","display_name":"Ambiguity","level":2,"score":0.6602654457092285},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.597796618938446},{"id":"https://openalex.org/C2777936996","wikidata":"https://www.wikidata.org/wiki/Q17148461","display_name":"Conformational ensembles","level":3,"score":0.5004079341888428},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.47117215394973755},{"id":"https://openalex.org/C2989108626","wikidata":"https://www.wikidata.org/wiki/Q904407","display_name":"Drug target","level":2,"score":0.4329261779785156},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4305740296840668},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.41637319326400757},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.36441701650619507},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.32151907682418823},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2231004238128662},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1711527407169342},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006863","descriptor_name":"Hydrogen-Ion Concentration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006863","descriptor_name":"Hydrogen-Ion Concentration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006863","descriptor_name":"Hydrogen-Ion Concentration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006863","descriptor_name":"Hydrogen-Ion Concentration","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":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"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":true},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.4c01612","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01612","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:39681511","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39681511","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}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":81,"referenced_works":["https://openalex.org/W1854810044","https://openalex.org/W1895007034","https://openalex.org/W1968356159","https://openalex.org/W1971731590","https://openalex.org/W1974438278","https://openalex.org/W1981747417","https://openalex.org/W1987114890","https://openalex.org/W1989753444","https://openalex.org/W1991683855","https://openalex.org/W1993177346","https://openalex.org/W1994713811","https://openalex.org/W2003582562","https://openalex.org/W2004792969","https://openalex.org/W2011207690","https://openalex.org/W2015039299","https://openalex.org/W2026418335","https://openalex.org/W2031674548","https://openalex.org/W2035123822","https://openalex.org/W2037652830","https://openalex.org/W2038444670","https://openalex.org/W2043383571","https://openalex.org/W2044529125","https://openalex.org/W2048681341","https://openalex.org/W2055719699","https://openalex.org/W2064298888","https://openalex.org/W2073356108","https://openalex.org/W2074112877","https://openalex.org/W2081771891","https://openalex.org/W2094795801","https://openalex.org/W2102713507","https://openalex.org/W2106748348","https://openalex.org/W2110334158","https://openalex.org/W2112620326","https://openalex.org/W2121234985","https://openalex.org/W2129019768","https://openalex.org/W2134599979","https://openalex.org/W2140173035","https://openalex.org/W2149655632","https://openalex.org/W2153231863","https://openalex.org/W2154670681","https://openalex.org/W2155267446","https://openalex.org/W2156016724","https://openalex.org/W2162343852","https://openalex.org/W2265102996","https://openalex.org/W2278873272","https://openalex.org/W2282949853","https://openalex.org/W2342981640","https://openalex.org/W2343931134","https://openalex.org/W2552522590","https://openalex.org/W2560705618","https://openalex.org/W2560915683","https://openalex.org/W2569540328","https://openalex.org/W2620747940","https://openalex.org/W2730519791","https://openalex.org/W2762430981","https://openalex.org/W2779060209","https://openalex.org/W2806783543","https://openalex.org/W2883855874","https://openalex.org/W2909674173","https://openalex.org/W2914978878","https://openalex.org/W2969663069","https://openalex.org/W2981948585","https://openalex.org/W3014501695","https://openalex.org/W3034934060","https://openalex.org/W3054319032","https://openalex.org/W3080583403","https://openalex.org/W3087004338","https://openalex.org/W3090513030","https://openalex.org/W3094648899","https://openalex.org/W3158740412","https://openalex.org/W3203204467","https://openalex.org/W4226013321","https://openalex.org/W4244247203","https://openalex.org/W4291020694","https://openalex.org/W4294679529","https://openalex.org/W4322732093","https://openalex.org/W4376129086","https://openalex.org/W4377565353","https://openalex.org/W4386758251","https://openalex.org/W4387639561","https://openalex.org/W4388539677"],"related_works":["https://openalex.org/W2553548503","https://openalex.org/W1967404732","https://openalex.org/W2226749982","https://openalex.org/W3045995536","https://openalex.org/W1968386238","https://openalex.org/W3206915023","https://openalex.org/W4308253407","https://openalex.org/W4310831746","https://openalex.org/W2119629574","https://openalex.org/W2059608951"],"abstract_inverted_index":{"As":[0],"the":[1,10,37,53],"name":[2],"implies,":[3],"structure-based":[4],"drug":[5,77],"design":[6],"requires":[7],"confidence":[8],"in":[9,51,60,87],"holo":[11],"complex":[12],"structure.":[13],"The":[14],"ability":[15],"to":[16,21,112],"clarify":[17],"which":[18],"protein":[19,55,113],"conformation":[20,56],"use":[22],"when":[23],"ambiguity":[24],"arises":[25],"would":[26],"be":[27],"incredibly":[28],"useful.":[29],"We":[30,101],"present":[31],"a":[32,107],"large":[33],"scale":[34],"validation":[35],"of":[36,106],"computational":[38],"method":[39],"Protein":[40],"Reorganization":[41],"Free":[42],"Energy":[43],"Perturbation":[44],"(PReorg-FEP)":[45],"and":[46,96],"demonstrate":[47],"its":[48],"quantitative":[49],"accuracy":[50],"selecting":[52],"correct":[54],"among":[57],"candidate":[58,71],"models":[59],"apo":[61],"or":[62],"ligand":[63],"induced":[64,83],"states":[65],"for":[66],"14":[67],"different":[68],"systems.":[69],"These":[70],"conformations":[72,82],"are":[73],"pulled":[74],"from":[75],"various":[76],"discovery":[78],"related":[79],"campaigns:":[80],"cryptic":[81],"by":[84],"novel":[85],"hits":[86],"lead":[88,94],"identification,":[89],"binding":[90],"site":[91],"rearrangement":[92],"during":[93],"optimization,":[95],"conflicting":[97],"structural":[98],"biology":[99],"models.":[100],"also":[102],"show":[103],"an":[104],"example":[105],"pH-dependent":[108],"conformational":[109],"change,":[110],"relevant":[111],"design.":[114]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-05-14T08:36:36.166977","created_date":"2025-10-10T00:00:00"}
