{"id":"https://openalex.org/W1968993610","doi":"https://doi.org/10.1371/journal.pcbi.1002131","title":"Binding Free Energy Landscape of Domain-Peptide Interactions","display_name":"Binding Free Energy Landscape of Domain-Peptide Interactions","publication_year":2011,"publication_date":"2011-08-18","ids":{"openalex":"https://openalex.org/W1968993610","doi":"https://doi.org/10.1371/journal.pcbi.1002131","mag":"1968993610","pmid":"https://pubmed.ncbi.nlm.nih.gov/21876662"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1002131","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1002131","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002131&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002131&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5083811644","display_name":"Iskra Staneva","orcid":null},"institutions":[{"id":"https://openalex.org/I187531555","display_name":"Lund University","ror":"https://ror.org/012a77v79","country_code":"SE","type":"education","lineage":["https://openalex.org/I187531555"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Iskra Staneva","raw_affiliation_strings":["Department of Astronomy and Theoretical Physics, Computational Biology and Biological Physics Group, Lund University, Lund, Sweden"],"affiliations":[{"raw_affiliation_string":"Department of Astronomy and Theoretical Physics, Computational Biology and Biological Physics Group, Lund University, Lund, Sweden","institution_ids":["https://openalex.org/I187531555"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5011206268","display_name":"Stefan Wallin","orcid":"https://orcid.org/0000-0002-1077-5331"},"institutions":[{"id":"https://openalex.org/I187531555","display_name":"Lund University","ror":"https://ror.org/012a77v79","country_code":"SE","type":"education","lineage":["https://openalex.org/I187531555"]}],"countries":["SE"],"is_corresponding":true,"raw_author_name":"Stefan Wallin","raw_affiliation_strings":["Department of Astronomy and Theoretical Physics, Computational Biology and Biological Physics Group, Lund University, Lund, Sweden"],"affiliations":[{"raw_affiliation_string":"Department of Astronomy and Theoretical Physics, Computational Biology and Biological Physics Group, Lund University, Lund, Sweden","institution_ids":["https://openalex.org/I187531555"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5011206268"],"corresponding_institution_ids":["https://openalex.org/I187531555"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.6006,"has_fulltext":true,"cited_by_count":19,"citation_normalized_percentile":{"value":0.82026199,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"7","issue":"8","first_page":"e1002131","last_page":"e1002131"},"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":0.9965999722480774,"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":0.9959999918937683,"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/pdz-domain","display_name":"PDZ domain","score":0.9370468854904175},{"id":"https://openalex.org/keywords/peptide","display_name":"Peptide","score":0.6499950885772705},{"id":"https://openalex.org/keywords/binding-energy","display_name":"Binding energy","score":0.5461883544921875},{"id":"https://openalex.org/keywords/plasma-protein-binding","display_name":"Plasma protein binding","score":0.5428289771080017},{"id":"https://openalex.org/keywords/binding-domain","display_name":"Binding domain","score":0.5402997732162476},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.5261259078979492},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.5052679181098938},{"id":"https://openalex.org/keywords/receptor\u2013ligand-kinetics","display_name":"Receptor\u2013ligand kinetics","score":0.4386351406574249},{"id":"https://openalex.org/keywords/binding-selectivity","display_name":"Binding selectivity","score":0.42223846912384033},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3944423794746399},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.3678349256515503},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3320184648036957},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.2879346013069153},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.22146645188331604},{"id":"https://openalex.org/keywords/atomic-physics","display_name":"Atomic physics","score":0.10660609602928162}],"concepts":[{"id":"https://openalex.org/C154428179","wikidata":"https://www.wikidata.org/wiki/Q24721050","display_name":"PDZ domain","level":2,"score":0.9370468854904175},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.6499950885772705},{"id":"https://openalex.org/C93282013","wikidata":"https://www.wikidata.org/wiki/Q420754","display_name":"Binding energy","level":2,"score":0.5461883544921875},{"id":"https://openalex.org/C51639874","wikidata":"https://www.wikidata.org/wiki/Q167149","display_name":"Plasma protein binding","level":2,"score":0.5428289771080017},{"id":"https://openalex.org/C25166345","wikidata":"https://www.wikidata.org/wiki/Q4914012","display_name":"Binding domain","level":3,"score":0.5402997732162476},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.5261259078979492},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.5052679181098938},{"id":"https://openalex.org/C152900378","wikidata":"https://www.wikidata.org/wiki/Q7302366","display_name":"Receptor\u2013ligand kinetics","level":3,"score":0.4386351406574249},{"id":"https://openalex.org/C96739231","wikidata":"https://www.wikidata.org/wiki/Q4914025","display_name":"Binding selectivity","level":2,"score":0.42223846912384033},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3944423794746399},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.3678349256515503},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3320184648036957},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.2879346013069153},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.22146645188331604},{"id":"https://openalex.org/C184779094","wikidata":"https://www.wikidata.org/wiki/Q26383","display_name":"Atomic physics","level":1,"score":0.10660609602928162},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","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":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":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":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054731","descriptor_name":"PDZ Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054731","descriptor_name":"PDZ Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054731","descriptor_name":"PDZ Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":8,"locations":[{"id":"doi:10.1371/journal.pcbi.1002131","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1002131","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002131&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmid:21876662","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21876662","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.288.8316","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.288.8316","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/55/bc/PLoS_Comput_Biol_2011_Aug_18_7(8)_e1002131.tar.gz","raw_type":"text"},{"id":"pmh:oai:RePEc:plo:pcbi00:1002131","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002131","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:56712f997269486cbed537dc48fc7246","is_oa":true,"landing_page_url":"https://doaj.org/article/56712f997269486cbed537dc48fc7246","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 7, Iss 8, p e1002131 (2011)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2166633","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3158039","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"},{"id":"pmh:oai:figshare.com:article/134107","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/Binding_Free_Energy_Landscape_of_Domain_Peptide_Interactions/134107","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"Dataset"},{"id":"pmh:oai:lup.lub.lu.se:2d1d1258-5f27-4717-b6c1-76b5806464f6","is_oa":false,"landing_page_url":"https://lup.lub.lu.se/record/2159131","pdf_url":null,"source":{"id":"https://openalex.org/S4306400536","display_name":"Lund University Publications (Lund University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I187531555","host_organization_name":"Lund University","host_organization_lineage":["https://openalex.org/I187531555"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ISSN: 1553-7358","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1002131","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1002131","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002131&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.8999999761581421,"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320322581","display_name":"Vetenskapsr\u00e5det","ror":"https://ror.org/03zttf063"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1968993610.pdf","grobid_xml":"https://content.openalex.org/works/W1968993610.grobid-xml"},"referenced_works_count":65,"referenced_works":["https://openalex.org/W265943136","https://openalex.org/W1524608481","https://openalex.org/W1858789161","https://openalex.org/W1963744170","https://openalex.org/W1983142511","https://openalex.org/W1983628095","https://openalex.org/W1996320892","https://openalex.org/W1997167217","https://openalex.org/W2001828594","https://openalex.org/W2006192061","https://openalex.org/W2009503206","https://openalex.org/W2010022403","https://openalex.org/W2015117663","https://openalex.org/W2018596625","https://openalex.org/W2019011769","https://openalex.org/W2023231003","https://openalex.org/W2023272942","https://openalex.org/W2027384625","https://openalex.org/W2032825057","https://openalex.org/W2037802250","https://openalex.org/W2041449172","https://openalex.org/W2053939374","https://openalex.org/W2057482592","https://openalex.org/W2058125583","https://openalex.org/W2059942519","https://openalex.org/W2059947046","https://openalex.org/W2060287439","https://openalex.org/W2062217029","https://openalex.org/W2063092201","https://openalex.org/W2065989745","https://openalex.org/W2068386918","https://openalex.org/W2071036069","https://openalex.org/W2074570440","https://openalex.org/W2087795016","https://openalex.org/W2089435371","https://openalex.org/W2096914244","https://openalex.org/W2096994057","https://openalex.org/W2101444664","https://openalex.org/W2102983156","https://openalex.org/W2105006060","https://openalex.org/W2113030357","https://openalex.org/W2115273980","https://openalex.org/W2116890528","https://openalex.org/W2121723608","https://openalex.org/W2122664553","https://openalex.org/W2123334353","https://openalex.org/W2126273386","https://openalex.org/W2127325055","https://openalex.org/W2130479394","https://openalex.org/W2130497867","https://openalex.org/W2131089409","https://openalex.org/W2133167066","https://openalex.org/W2136513242","https://openalex.org/W2140933450","https://openalex.org/W2143264455","https://openalex.org/W2145080853","https://openalex.org/W2148441993","https://openalex.org/W2152854378","https://openalex.org/W2157693914","https://openalex.org/W2161668221","https://openalex.org/W2162685411","https://openalex.org/W2163336852","https://openalex.org/W2170117113","https://openalex.org/W2329867073","https://openalex.org/W3098405609"],"related_works":["https://openalex.org/W2087603047","https://openalex.org/W2042926683","https://openalex.org/W2022403117","https://openalex.org/W2038514743","https://openalex.org/W3167168557","https://openalex.org/W1993238323","https://openalex.org/W2000251153","https://openalex.org/W2001828594","https://openalex.org/W4224290510","https://openalex.org/W1968993610"],"abstract_inverted_index":{"Peptide":[0],"recognition":[1],"domains":[2,7,66,96,153],"(PRDs)":[3],"are":[4,21,105,239],"ubiquitous":[5],"protein":[6,13],"which":[8,102,246],"mediate":[9],"large":[10,46,210],"numbers":[11],"of":[12,42,212],"interactions":[14],"in":[15,27,101,144,200,245,253],"the":[16,38,88,103,110,119,145,148,160,168,228,247],"cell.":[17],"How":[18],"these":[19],"PRDs":[20],"able":[22],"to":[23,182,233],"recognize":[24],"peptide":[25,39,248],"sequences":[26],"a":[28,45,78,84,98,129,135,183,209,242],"rapid":[29],"and":[30,73,192,195],"specific":[31],"manner":[32],"is":[33,62,92,164],"incompletely":[34],"understood.":[35],"We":[36,139],"explore":[37],"binding":[40,79,99,112,126,156,202,218,225,243],"process":[41,100],"PDZ":[43,65,70,111,184],"domains,":[44,77],"PRD":[47],"family,":[48],"from":[49],"an":[50,54,197,254],"equilibrium":[51],"perspective":[52],"using":[53],"all-atom":[55],"Monte":[56],"Carlo":[57],"(MC)":[58],"approach.":[59],"Our":[60,236],"focus":[61],"two":[63,68,149],"different":[64],"representing":[67],"major":[69],"classes,":[71],"I":[72,162,191],"II.":[74,172],"For":[75],"both":[76,95,152],"free":[80,157,203],"energy":[81,158,204],"surface":[82],"with":[83,118,123,186,241],"strong":[85],"bias":[86],"toward":[87],"native":[89],"bound":[90,108],"state":[91],"found.":[93],"Moreover,":[94],"exhibit":[97,154],"peptides":[104],"mostly":[106],"either":[107],"at":[109],"pocket":[113],"or":[114],"else":[115],"interact":[116],"little":[117],"domain":[120,185,231],"surface.":[121],"Consistent":[122],"this,":[124],"various":[125],"observables":[127],"show":[128],"temperature":[130],"dependence":[131],"well":[132],"described":[133],"by":[134],"simple":[136],"two-state":[137],"model.":[138],"also":[140],"find":[141,196],"important":[142],"differences":[143],"details":[146],"between":[147],"domains.":[150],"While":[151],"well-defined":[155],"barriers,":[159],"class":[161,171,190,229,234],"barrier":[163],"significantly":[165,223],"weaker":[166],"than":[167],"one":[169],"for":[170,189,227],"To":[173],"probe":[174],"this":[175],"issue":[176],"further,":[177],"we":[178,207],"apply":[179],"our":[180],"method":[181],"dual":[187],"specificity":[188],"II":[193,230],"peptides,":[194],"analogous":[198],"difference":[199],"their":[201],"barriers.":[205],"Lastly,":[206],"perform":[208],"number":[211],"fixed-temperature":[213],"MC":[214],"kinetics":[215],"trajectories":[216,221],"under":[217],"conditions.":[219],"These":[220],"reveal":[222],"slower":[224],"dynamics":[226],"relative":[232],"I.":[235],"combined":[237],"results":[238],"consistent":[240],"mechanism":[244],"C":[249],"terminal":[250],"residue":[251],"binds":[252],"initial,":[255],"rate-limiting":[256],"step.":[257]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":8}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}