{"id":"https://openalex.org/W4281678062","doi":"https://doi.org/10.1021/acs.jcim.2c00348","title":"Alchemical Free Energy Calculations to Investigate Protein\u2013Protein Interactions: the Case of the CDC42/PAK1 Complex","display_name":"Alchemical Free Energy Calculations to Investigate Protein\u2013Protein Interactions: the Case of the CDC42/PAK1 Complex","publication_year":2022,"publication_date":"2022-06-09","ids":{"openalex":"https://openalex.org/W4281678062","doi":"https://doi.org/10.1021/acs.jcim.2c00348","pmid":"https://pubmed.ncbi.nlm.nih.gov/35679463"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.2c00348","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c00348","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.2c00348","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","license_id":"https://openalex.org/licenses/cc-by","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.2c00348","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5073005132","display_name":"Maria Antonietta La Serra","orcid":"https://orcid.org/0000-0001-8732-9965"},"institutions":[{"id":"https://openalex.org/I30771326","display_name":"Italian Institute of Technology","ror":"https://ror.org/042t93s57","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Maria Antonietta La Serra","raw_affiliation_strings":["Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, via Morego 30, Genoa 16163, Italy"],"raw_orcid":"https://orcid.org/0000-0001-8732-9965","affiliations":[{"raw_affiliation_string":"Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, via Morego 30, Genoa 16163, Italy","institution_ids":["https://openalex.org/I30771326"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000266480","display_name":"Pietro Vidossich","orcid":null},"institutions":[{"id":"https://openalex.org/I30771326","display_name":"Italian Institute of Technology","ror":"https://ror.org/042t93s57","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Pietro Vidossich","raw_affiliation_strings":["Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, via Morego 30, Genoa 16163, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, via Morego 30, Genoa 16163, Italy","institution_ids":["https://openalex.org/I30771326"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090137290","display_name":"Isabella Maria Acquistapace","orcid":"https://orcid.org/0000-0002-5820-7683"},"institutions":[{"id":"https://openalex.org/I30771326","display_name":"Italian Institute of Technology","ror":"https://ror.org/042t93s57","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Isabella Acquistapace","raw_affiliation_strings":["Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, via Morego 30, Genoa 16163, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, via Morego 30, Genoa 16163, Italy","institution_ids":["https://openalex.org/I30771326"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078269386","display_name":"Anand K. Ganesan","orcid":"https://orcid.org/0000-0003-4944-9274"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anand K. Ganesan","raw_affiliation_strings":["Department of Biological Chemistry, University of California, Irvine, Irvine, California 92697, United States","Department of Dermatology, University of California, Irvine, Irvine, California 92697, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Chemistry, University of California, Irvine, Irvine, California 92697, United States","institution_ids":["https://openalex.org/I204250578"]},{"raw_affiliation_string":"Department of Dermatology, University of California, Irvine, Irvine, California 92697, United States","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062592876","display_name":"Marco De Vivo","orcid":"https://orcid.org/0000-0003-4022-5661"},"institutions":[{"id":"https://openalex.org/I30771326","display_name":"Italian Institute of Technology","ror":"https://ror.org/042t93s57","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Marco De Vivo","raw_affiliation_strings":["Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, via Morego 30, Genoa 16163, Italy"],"raw_orcid":"https://orcid.org/0000-0003-4022-5661","affiliations":[{"raw_affiliation_string":"Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, via Morego 30, Genoa 16163, Italy","institution_ids":["https://openalex.org/I30771326"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5062592876"],"corresponding_institution_ids":["https://openalex.org/I30771326"],"apc_list":null,"apc_paid":null,"fwci":1.3867,"has_fulltext":false,"cited_by_count":21,"citation_normalized_percentile":{"value":0.80459993,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"62","issue":"12","first_page":"3023","last_page":"3033"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9993000030517578,"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":0.9993000030517578,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.996999979019165,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9945999979972839,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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"}}],"keywords":[{"id":"https://openalex.org/keywords/cdc42","display_name":"CDC42","score":0.7525101900100708},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6656812429428101},{"id":"https://openalex.org/keywords/mutagenesis","display_name":"Mutagenesis","score":0.5796262621879578},{"id":"https://openalex.org/keywords/threonine","display_name":"Threonine","score":0.46417924761772156},{"id":"https://openalex.org/keywords/effector","display_name":"Effector","score":0.4321298599243164},{"id":"https://openalex.org/keywords/serine","display_name":"Serine","score":0.4217830002307892},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.4102972447872162},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3968006670475006},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3751637637615204},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.36670446395874023},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3217606842517853},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.3122071921825409},{"id":"https://openalex.org/keywords/gtpase","display_name":"GTPase","score":0.3114722669124603},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.30469810962677},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.2581699788570404},{"id":"https://openalex.org/keywords/phosphorylation","display_name":"Phosphorylation","score":0.16012197732925415},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10870778560638428}],"concepts":[{"id":"https://openalex.org/C2780040266","wikidata":"https://www.wikidata.org/wiki/Q15311701","display_name":"CDC42","level":3,"score":0.7525101900100708},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6656812429428101},{"id":"https://openalex.org/C16318435","wikidata":"https://www.wikidata.org/wiki/Q149299","display_name":"Mutagenesis","level":4,"score":0.5796262621879578},{"id":"https://openalex.org/C2775880066","wikidata":"https://www.wikidata.org/wiki/Q186521","display_name":"Threonine","level":4,"score":0.46417924761772156},{"id":"https://openalex.org/C51785407","wikidata":"https://www.wikidata.org/wiki/Q2627568","display_name":"Effector","level":2,"score":0.4321298599243164},{"id":"https://openalex.org/C2776414213","wikidata":"https://www.wikidata.org/wiki/Q183290","display_name":"Serine","level":3,"score":0.4217830002307892},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.4102972447872162},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3968006670475006},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3751637637615204},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.36670446395874023},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3217606842517853},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.3122071921825409},{"id":"https://openalex.org/C207332259","wikidata":"https://www.wikidata.org/wiki/Q769143","display_name":"GTPase","level":2,"score":0.3114722669124603},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.30469810962677},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.2581699788570404},{"id":"https://openalex.org/C11960822","wikidata":"https://www.wikidata.org/wiki/Q242736","display_name":"Phosphorylation","level":2,"score":0.16012197732925415},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10870778560638428},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016296","descriptor_name":"Mutagenesis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016296","descriptor_name":"Mutagenesis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016296","descriptor_name":"Mutagenesis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016296","descriptor_name":"Mutagenesis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017346","descriptor_name":"Protein Serine-Threonine Kinases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017346","descriptor_name":"Protein Serine-Threonine Kinases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017346","descriptor_name":"Protein Serine-Threonine Kinases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017346","descriptor_name":"Protein Serine-Threonine Kinases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054462","descriptor_name":"p21-Activated Kinases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D054462","descriptor_name":"p21-Activated Kinases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D054462","descriptor_name":"p21-Activated Kinases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D054462","descriptor_name":"p21-Activated Kinases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1021/acs.jcim.2c00348","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c00348","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.2c00348","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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:35679463","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35679463","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:ark:/13030/qt6m3780w9","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:escholarship.org:ark:/13030/qt6m3780w9","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/6m3780w9","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"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":"Journal of Chemical Information and Modeling, vol 62, iss 12","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9241073","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9241073","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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.2c00348","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c00348","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.2c00348","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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","score":0.8999999761581421,"display_name":"Affordable and clean energy"}],"awards":[{"id":"https://openalex.org/G2178217092","display_name":null,"funder_award_id":"R01CA244571","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G2450012508","display_name":null,"funder_award_id":"IG23679","funder_id":"https://openalex.org/F4320323054","funder_display_name":"Associazione Italiana per la Ricerca sul Cancro"}],"funders":[{"id":"https://openalex.org/F4320323054","display_name":"Associazione Italiana per la Ricerca sul Cancro","ror":"https://ror.org/02g2x7380"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4281678062.pdf","grobid_xml":"https://content.openalex.org/works/W4281678062.grobid-xml"},"referenced_works_count":73,"referenced_works":["https://openalex.org/W129136316","https://openalex.org/W582864414","https://openalex.org/W1153842025","https://openalex.org/W1556106311","https://openalex.org/W1968984443","https://openalex.org/W1969046853","https://openalex.org/W1969350101","https://openalex.org/W1969836007","https://openalex.org/W1970973025","https://openalex.org/W1974420063","https://openalex.org/W1976499671","https://openalex.org/W1980618423","https://openalex.org/W1981225934","https://openalex.org/W1991667171","https://openalex.org/W2003519013","https://openalex.org/W2008174310","https://openalex.org/W2017829285","https://openalex.org/W2019574809","https://openalex.org/W2019731805","https://openalex.org/W2019851613","https://openalex.org/W2023612761","https://openalex.org/W2024598372","https://openalex.org/W2025006523","https://openalex.org/W2027404256","https://openalex.org/W2028841370","https://openalex.org/W2040567131","https://openalex.org/W2042655455","https://openalex.org/W2060297361","https://openalex.org/W2063206968","https://openalex.org/W2065283382","https://openalex.org/W2073439264","https://openalex.org/W2078823941","https://openalex.org/W2087574732","https://openalex.org/W2091169894","https://openalex.org/W2102312968","https://openalex.org/W2105103540","https://openalex.org/W2110845720","https://openalex.org/W2129277563","https://openalex.org/W2154670681","https://openalex.org/W2156571424","https://openalex.org/W2160807621","https://openalex.org/W2161340336","https://openalex.org/W2165835468","https://openalex.org/W2271736303","https://openalex.org/W2312831416","https://openalex.org/W2404280981","https://openalex.org/W2549686806","https://openalex.org/W2558870009","https://openalex.org/W2560233715","https://openalex.org/W2625293850","https://openalex.org/W2772606519","https://openalex.org/W2782230450","https://openalex.org/W2788194767","https://openalex.org/W2791485121","https://openalex.org/W2793266825","https://openalex.org/W2800994818","https://openalex.org/W2808890768","https://openalex.org/W2898221567","https://openalex.org/W2911615806","https://openalex.org/W2950669909","https://openalex.org/W2951718918","https://openalex.org/W3008905875","https://openalex.org/W3014067025","https://openalex.org/W3022466913","https://openalex.org/W3034934060","https://openalex.org/W3054319032","https://openalex.org/W3080583403","https://openalex.org/W3087004338","https://openalex.org/W3087769169","https://openalex.org/W3174693957","https://openalex.org/W4212959738","https://openalex.org/W4225665241","https://openalex.org/W4252893650"],"related_works":["https://openalex.org/W146073455","https://openalex.org/W2067854585","https://openalex.org/W1981086346","https://openalex.org/W1993181715","https://openalex.org/W1974420063","https://openalex.org/W1503951074","https://openalex.org/W4328116740","https://openalex.org/W2080304943","https://openalex.org/W2040571096","https://openalex.org/W2321910107"],"abstract_inverted_index":{"Here,":[0],"we":[1,23,71,93],"show":[2,95],"that":[3,96,125],"alchemical":[4,126],"free":[5,127],"energy":[6,128],"calculations":[7,129],"can":[8,109,130],"quantitatively":[9],"compute":[10],"the":[11,16,26,31,44,77,101,105,112,135],"effect":[12],"of":[13,50,58,100,137],"mutations":[14,75],"at":[15],"protein-protein":[17],"interface.":[18],"As":[19],"a":[20,40,48,97],"test":[21],"case,":[22],"have":[24,72],"used":[25],"protein":[27],"complex":[28,46,79],"formed":[29],"by":[30],"small":[32],"Rho-GTPase":[33],"CDC42":[34],"and":[35,53,65,80,86],"its":[36,59],"downstream":[37],"effector":[38],"PAK1,":[39],"serine/threonine":[41],"kinase.":[42],"Notably,":[43],"CDC42/PAK1":[45,78],"offers":[47],"wealth":[49],"structural,":[51],"mutagenesis,":[52],"binding":[54,90],"affinity":[55],"data":[56,88],"because":[57],"central":[60],"role":[61],"in":[62,76,104],"cellular":[63],"signaling":[64],"cancer":[66],"progression.":[67],"In":[68],"this":[69,122],"context,":[70],"considered":[73],"16":[74],"obtained":[81],"excellent":[82],"agreement":[83],"between":[84],"computed":[85,113],"experimental":[87,138],"on":[89],"affinity.":[91],"Importantly,":[92],"also":[94],"careful":[98],"analysis":[99],"side-chain":[102],"conformations":[103],"mutated":[106],"amino":[107],"acids":[108],"considerably":[110],"improve":[111],"estimates,":[114],"solving":[115],"issues":[116],"related":[117],"to":[118],"sampling":[119],"limitations.":[120],"Overall,":[121],"study":[123],"demonstrates":[124],"conveniently":[131],"be":[132],"integrated":[133],"into":[134],"design":[136],"mutagenesis":[139],"studies.":[140]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":2}],"updated_date":"2026-05-05T08:41:31.759640","created_date":"2025-10-10T00:00:00"}