{"id":"https://openalex.org/W4413831186","doi":"https://doi.org/10.26434/chemrxiv-2025-cc60b-v2","title":"Predicting the thermodynamics and kinetics of protein-protein interaction from spontaneous association simulations","display_name":"Predicting the thermodynamics and kinetics of protein-protein interaction from spontaneous association simulations","publication_year":2025,"publication_date":"2025-08-29","ids":{"openalex":"https://openalex.org/W4413831186","doi":"https://doi.org/10.26434/chemrxiv-2025-cc60b-v2"},"language":"en","primary_location":{"id":"doi:10.26434/chemrxiv-2025-cc60b-v2","doi":"https://doi.org/10.26434/chemrxiv-2025-cc60b-v2","is_oa":true,"landing_page_url":"https://doi.org/10.26434/chemrxiv-2025-cc60b-v2","pdf_url":null,"source":{"id":"https://openalex.org/S4393918830","display_name":"ChemRxiv","issn_l":"2573-2293","issn":["2573-2293"],"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},"volume":null,"type":"preprint","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.26434/chemrxiv-2025-cc60b-v2","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5063356130","display_name":"Line Mouaffac","orcid":"https://orcid.org/0009-0003-3027-6825","observed_orcids":["https://orcid.org/0009-0003-3027-6825"]},"institutions":[{"id":"https://openalex.org/I39804081","display_name":"Sorbonne Universit\u00e9","ror":"https://ror.org/02en5vm52","country_code":"FR","type":"education","lineage":["https://openalex.org/I39804081"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Line Mouaffac","raw_affiliation_strings":["Sorbonne Universit\u00e9"],"raw_orcid":"https://orcid.org/0009-0003-3027-6825","affiliations":[{"raw_affiliation_string":"Sorbonne Universit\u00e9","institution_ids":["https://openalex.org/I39804081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074880338","display_name":"Karen Palacio\u2010Rodr\u00edguez","orcid":"https://orcid.org/0000-0003-4327-8478","observed_orcids":["https://orcid.org/0000-0003-4327-8478"]},"institutions":[{"id":"https://openalex.org/I4210124035","display_name":"Max Planck Institute of Biophysics","ror":"https://ror.org/02panr271","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210124035"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Karen Palacio Rodriguez","raw_affiliation_strings":["Max Planck Institute for Biophysics"],"raw_orcid":"https://orcid.org/0000-0003-4327-8478","affiliations":[{"raw_affiliation_string":"Max Planck Institute for Biophysics","institution_ids":["https://openalex.org/I4210124035"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044840019","display_name":"Alessandro Barducci","orcid":"https://orcid.org/0000-0002-1911-8039","observed_orcids":["https://orcid.org/0000-0002-1911-8039"]},"institutions":[{"id":"https://openalex.org/I19894307","display_name":"Universit\u00e9 de Montpellier","ror":"https://ror.org/051escj72","country_code":"FR","type":"education","lineage":["https://openalex.org/I19894307"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Alessandro Barducci","raw_affiliation_strings":["Universit\u00e9 de Montpellier"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universit\u00e9 de Montpellier","institution_ids":["https://openalex.org/I19894307"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065938694","display_name":"Peter G. Bolhuis","orcid":"https://orcid.org/0000-0002-3698-9258","observed_orcids":["https://orcid.org/0000-0002-3698-9258"]},"institutions":[{"id":"https://openalex.org/I887064364","display_name":"University of Amsterdam","ror":"https://ror.org/04dkp9463","country_code":"NL","type":"education","lineage":["https://openalex.org/I887064364"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Peter Bolhuis","raw_affiliation_strings":["University of Amsterdam"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Amsterdam","institution_ids":["https://openalex.org/I887064364"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083064307","display_name":"Isabelle Callebaut","orcid":"https://orcid.org/0000-0003-3124-887X","observed_orcids":["https://orcid.org/0000-0003-3124-887X"]},"institutions":[{"id":"https://openalex.org/I39804081","display_name":"Sorbonne Universit\u00e9","ror":"https://ror.org/02en5vm52","country_code":"FR","type":"education","lineage":["https://openalex.org/I39804081"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Isabelle Callebaut","raw_affiliation_strings":["Sorbonne Universit\u00e9"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Sorbonne Universit\u00e9","institution_ids":["https://openalex.org/I39804081"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015296013","display_name":"Fabio Pietrucci","orcid":"https://orcid.org/0000-0002-4892-2667","observed_orcids":["https://orcid.org/0000-0002-4892-2667"]},"institutions":[{"id":"https://openalex.org/I39804081","display_name":"Sorbonne Universit\u00e9","ror":"https://ror.org/02en5vm52","country_code":"FR","type":"education","lineage":["https://openalex.org/I39804081"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Fabio Pietrucci","raw_affiliation_strings":["Sorbonne Universit\u00e9"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Sorbonne Universit\u00e9","institution_ids":["https://openalex.org/I39804081"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9907000064849854,"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":0.9907000064849854,"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/T12044","display_name":"Advanced Physical and Chemical Molecular Interactions","score":0.005200000014156103,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.0012000000569969416,"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/protein-protein-interaction","display_name":"protein-protein interaction","score":0.9269999861717224},{"id":"https://openalex.org/keywords/dissociation-free-energy","display_name":"dissociation free energy","score":0.875},{"id":"https://openalex.org/keywords/dissociation-kinetics","display_name":"dissociation kinetics","score":0.7850000262260437},{"id":"https://openalex.org/keywords/binding-pathway","display_name":"binding pathway","score":0.6299999952316284},{"id":"https://openalex.org/keywords/langevin-model","display_name":"Langevin model","score":0.6880000233650208},{"id":"https://openalex.org/keywords/interface-residues","display_name":"interface residues","score":0.5730000138282776},{"id":"https://openalex.org/keywords/water-mediated-interactions","display_name":"water-mediated interactions","score":0.5920000076293945}],"concepts":[{"id":"https://openalex.org/C148898269","wikidata":"https://www.wikidata.org/wiki/Q1108792","display_name":"Kinetics","level":2,"score":0.7261486053466797},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.662372350692749},{"id":"https://openalex.org/C142853389","wikidata":"https://www.wikidata.org/wiki/Q744778","display_name":"Association (psychology)","level":2,"score":0.5132467746734619},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4991941452026367},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.19884330034255981},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.11659121513366699},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C542102704","wikidata":"https://www.wikidata.org/wiki/Q183257","display_name":"Psychotherapist","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.26434/chemrxiv-2025-cc60b-v2","doi":"https://doi.org/10.26434/chemrxiv-2025-cc60b-v2","is_oa":true,"landing_page_url":"https://doi.org/10.26434/chemrxiv-2025-cc60b-v2","pdf_url":null,"source":{"id":"https://openalex.org/S4393918830","display_name":"ChemRxiv","issn_l":"2573-2293","issn":["2573-2293"],"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.26434/chemrxiv-2025-cc60b-v2","doi":"https://doi.org/10.26434/chemrxiv-2025-cc60b-v2","is_oa":true,"landing_page_url":"https://doi.org/10.26434/chemrxiv-2025-cc60b-v2","pdf_url":null,"source":{"id":"https://openalex.org/S4393918830","display_name":"ChemRxiv","issn_l":"2573-2293","issn":["2573-2293"],"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},"sustainable_development_goals":[],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2899084033","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W4391375266","https://openalex.org/W2078814861","https://openalex.org/W2527526854","https://openalex.org/W1976181487"],"abstract_inverted_index":{"Despite":[0],"the":[1,38,45,49,63,69,72,77,101,124,127,137],"biological":[2],"and":[3,13,65,84,111,139],"pharmaceutical":[4],"importance":[5],"of":[6,29,41,51,68,118,130],"protein-protein":[7,131],"interactions,":[8,132],"accurately":[9],"predicting":[10],"dissociation":[11,87],"free-energies":[12],"rates":[14],"remains":[15],"an":[16],"outstanding":[17],"challenge.":[18],"Here,":[19],"we":[20,61],"predict":[21],"these":[22],"quantities":[23],"from":[24],"all-atom":[25],"molecular":[26,96],"dynamics":[27,97],"simulations":[28],"ribonuclease":[30],"barnase":[31],"with":[32,48],"its":[33],"inhibitor":[34],"barstar.":[35],"We":[36],"characterized":[37],"detailed":[39],"contribution":[40],"different":[42,81],"residues":[43],"at":[44],"interface,":[46],"along":[47],"role":[50],"water,":[52],"identifying":[53],"three":[54],"distinct":[55],"binding":[56],"pathways.":[57],"Using":[58],"Langevin":[59],"models,":[60],"inferred":[62],"free-energy":[64],"diffusion":[66],"landscape":[67],"process,":[70],"hence":[71],"kinetic":[73],"properties,":[74],"systematically":[75],"evaluating":[76],"model's":[78],"quality":[79],"across":[80],"collective":[82],"variables,":[83],"obtaining":[85],"robust":[86],"rate":[88],"predictions.":[89],"Our":[90],"computational":[91],"scheme,":[92],"based":[93],"on":[94,136],"unbiased":[95],"trajectories":[98],"initialized":[99],"in":[100],"dissociated":[102],"state,":[103],"is":[104,113],"significantly":[105],"simpler":[106],"than":[107],"previously":[108],"proposed":[109],"approaches,":[110],"it":[112],"very":[114],"data-efficient,":[115],"requiring":[116],"tens":[117],"sub-microsecond":[119],"simulations.":[120],"The":[121],"results":[122],"open":[123],"way":[125],"to":[126],"systematic":[128],"study":[129],"including":[133],"atomic-level":[134],"details":[135],"mechanism":[138],"kinetics":[140],"that":[141],"are":[142],"paramount":[143],"for":[144],"biomedical":[145],"applications.":[146]},"counts_by_year":[],"updated_date":"2026-09-23T05:00:35.095934","created_date":"2025-10-10T00:00:00"}
