{"id":"https://openalex.org/W7116757815","doi":"https://doi.org/10.1021/acs.jcim.5c02118","title":"Contact Parallel Cascade Selection Molecular Dynamics (cPaCS-MD) for Accurate In Silico Prediction of Peptide Binding Free Energy","display_name":"Contact Parallel Cascade Selection Molecular Dynamics (cPaCS-MD) for Accurate In Silico Prediction of Peptide Binding Free Energy","publication_year":2025,"publication_date":"2025-12-22","ids":{"openalex":"https://openalex.org/W7116757815","doi":"https://doi.org/10.1021/acs.jcim.5c02118","pmid":"https://pubmed.ncbi.nlm.nih.gov/41428857"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c02118","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c02118","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/A5029697744","display_name":"Viktor Prypoten","orcid":"https://orcid.org/0000-0002-2376-4455"},"institutions":[{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Viktor Prypoten","raw_affiliation_strings":["Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia"],"raw_orcid":"https://orcid.org/0000-0002-2376-4455","affiliations":[{"raw_affiliation_string":"Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia","institution_ids":["https://openalex.org/I56590836"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039797008","display_name":"Raymond S. Norton","orcid":"https://orcid.org/0000-0001-8893-0584"},"institutions":[{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Raymond S. Norton","raw_affiliation_strings":["Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia"],"raw_orcid":"https://orcid.org/0000-0001-8893-0584","affiliations":[{"raw_affiliation_string":"Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia","institution_ids":["https://openalex.org/I56590836"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027617278","display_name":"David K. Chalmers","orcid":"https://orcid.org/0000-0003-2366-569X"},"institutions":[{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"David K. Chalmers","raw_affiliation_strings":["Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia"],"raw_orcid":"https://orcid.org/0000-0003-2366-569X","affiliations":[{"raw_affiliation_string":"Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia","institution_ids":["https://openalex.org/I56590836"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5027617278"],"corresponding_institution_ids":["https://openalex.org/I56590836"],"apc_list":null,"apc_paid":null,"fwci":0.4868,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.70887105,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"66","issue":"1","first_page":"413","last_page":"424"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.5357000231742859,"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":0.5357000231742859,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.1282999962568283,"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"}},{"id":"https://openalex.org/T11103","display_name":"Antimicrobial Peptides and Activities","score":0.06870000064373016,"subfield":{"id":"https://openalex.org/subfields/2404","display_name":"Microbiology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.7402999997138977},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.7174000144004822},{"id":"https://openalex.org/keywords/peptide","display_name":"Peptide","score":0.6050999760627747},{"id":"https://openalex.org/keywords/cascade","display_name":"Cascade","score":0.593500018119812},{"id":"https://openalex.org/keywords/binding-affinities","display_name":"Binding affinities","score":0.5831000208854675},{"id":"https://openalex.org/keywords/affinities","display_name":"Affinities","score":0.524399995803833},{"id":"https://openalex.org/keywords/markov-chain","display_name":"Markov chain","score":0.4875999987125397},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.47360000014305115},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.38760000467300415}],"concepts":[{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.7402999997138977},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.7174000144004822},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.6050999760627747},{"id":"https://openalex.org/C34146451","wikidata":"https://www.wikidata.org/wiki/Q5048094","display_name":"Cascade","level":2,"score":0.593500018119812},{"id":"https://openalex.org/C3018795828","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Binding affinities","level":3,"score":0.5831000208854675},{"id":"https://openalex.org/C2780283098","wikidata":"https://www.wikidata.org/wiki/Q4688960","display_name":"Affinities","level":2,"score":0.524399995803833},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.4875999987125397},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.47360000014305115},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.46970000863075256},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.4219000041484833},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4162999987602234},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4065000116825104},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.38760000467300415},{"id":"https://openalex.org/C10803110","wikidata":"https://www.wikidata.org/wiki/Q1341441","display_name":"Force field (fiction)","level":2,"score":0.3531999886035919},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.34860000014305115},{"id":"https://openalex.org/C163836022","wikidata":"https://www.wikidata.org/wiki/Q6771326","display_name":"Markov model","level":3,"score":0.3456999957561493},{"id":"https://openalex.org/C140779682","wikidata":"https://www.wikidata.org/wiki/Q210868","display_name":"Sampling (signal processing)","level":3,"score":0.3433000147342682},{"id":"https://openalex.org/C66882249","wikidata":"https://www.wikidata.org/wiki/Q169336","display_name":"Homogeneous","level":2,"score":0.32109999656677246},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.32109999656677246},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.3010999858379364},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.2793000042438507},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.2757999897003174},{"id":"https://openalex.org/C51639874","wikidata":"https://www.wikidata.org/wiki/Q167149","display_name":"Plasma protein binding","level":2,"score":0.2687999904155731},{"id":"https://openalex.org/C128747166","wikidata":"https://www.wikidata.org/wiki/Q7881414","display_name":"Umbrella sampling","level":3,"score":0.2685000002384186},{"id":"https://openalex.org/C18762648","wikidata":"https://www.wikidata.org/wiki/Q42213","display_name":"Work (physics)","level":2,"score":0.26739999651908875},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.25519999861717224},{"id":"https://openalex.org/C2777735830","wikidata":"https://www.wikidata.org/wiki/Q6507061","display_name":"Molecular binding","level":3,"score":0.2547999918460846}],"mesh":[{"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":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","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":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"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":"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}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.5c02118","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c02118","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:41428857","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41428857","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":[{"display_name":"Affordable and clean energy","score":0.7233521938323975,"id":"https://metadata.un.org/sdg/7"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":74,"referenced_works":["https://openalex.org/W203363010","https://openalex.org/W1031578623","https://openalex.org/W1178456644","https://openalex.org/W1964758803","https://openalex.org/W1978633697","https://openalex.org/W1987327282","https://openalex.org/W1989277510","https://openalex.org/W1991794210","https://openalex.org/W1993177346","https://openalex.org/W2001996470","https://openalex.org/W2010193651","https://openalex.org/W2016033647","https://openalex.org/W2017196167","https://openalex.org/W2021520922","https://openalex.org/W2056211671","https://openalex.org/W2056617023","https://openalex.org/W2057477511","https://openalex.org/W2057806291","https://openalex.org/W2072256473","https://openalex.org/W2072820038","https://openalex.org/W2081693079","https://openalex.org/W2085213650","https://openalex.org/W2128572087","https://openalex.org/W2130479394","https://openalex.org/W2132262459","https://openalex.org/W2141273392","https://openalex.org/W2143592395","https://openalex.org/W2147988069","https://openalex.org/W2152813428","https://openalex.org/W2178878751","https://openalex.org/W2206954826","https://openalex.org/W2226825552","https://openalex.org/W2323410768","https://openalex.org/W2399447404","https://openalex.org/W2404280981","https://openalex.org/W2405075761","https://openalex.org/W2423210081","https://openalex.org/W2604733798","https://openalex.org/W2738737407","https://openalex.org/W2748401173","https://openalex.org/W2770896051","https://openalex.org/W2791485121","https://openalex.org/W2805823639","https://openalex.org/W2807273463","https://openalex.org/W2874062053","https://openalex.org/W2909251421","https://openalex.org/W2915248527","https://openalex.org/W2999469162","https://openalex.org/W3010340553","https://openalex.org/W3012536037","https://openalex.org/W3035076119","https://openalex.org/W3039774048","https://openalex.org/W3042908073","https://openalex.org/W3044187902","https://openalex.org/W3094004932","https://openalex.org/W3120960768","https://openalex.org/W3175314490","https://openalex.org/W3196587048","https://openalex.org/W4210860040","https://openalex.org/W4212959738","https://openalex.org/W4220881758","https://openalex.org/W4220970481","https://openalex.org/W4235602347","https://openalex.org/W4285043746","https://openalex.org/W4321083912","https://openalex.org/W4324129669","https://openalex.org/W4386438977","https://openalex.org/W4387326815","https://openalex.org/W4387334097","https://openalex.org/W4387639561","https://openalex.org/W4389076815","https://openalex.org/W4391223048","https://openalex.org/W4391821348","https://openalex.org/W4400850306"],"related_works":[],"abstract_inverted_index":{"Although":[0],"peptide":[1,42,61,82,146,155],"drugs":[2],"make":[3],"up":[4],"a":[5,37,69,87,151,163],"growing":[6],"proportion":[7],"of":[8,14,24,31,72,101,107,141,154,172,180],"the":[9,22,29,114,137,170,178],"pharmaceutical":[10],"market,":[11],"computational":[12,25],"prediction":[13],"peptide\u2013protein":[15,173],"binding":[16,62,83,147],"affinity":[17],"remains":[18],"challenging,":[19],"which":[20],"limits":[21],"use":[23],"methods":[26,143],"to":[27,68,113],"assist":[28,177],"optimization":[30],"bioactive":[32],"peptides.":[33],"We":[34,64,110,157],"have":[35,65],"developed":[36],"novel":[38],"method":[39,120],"for":[40,144,169,182],"modeling":[41],"unbinding,":[43],"designated":[44],"contact":[45],"parallel":[46],"cascade":[47],"selection":[48],"molecular":[49],"dynamics":[50],"(cPaCS-MD),":[51],"which,":[52],"when":[53],"combined":[54],"with":[55,86],"Markov":[56],"state":[57],"models,":[58],"accurately":[59],"predicts":[60,80],"affinities.":[63],"applied":[66],"cPaCS-MD":[67,112,160],"diverse":[70,152,183],"set":[71,153],"12":[73],"protein\u2013peptide":[74],"complexes":[75],"and":[76,95,104,121,129,166,175],"found":[77,122],"that":[78,123,149,159],"it":[79],"experimental":[81],"free":[84],"energies":[85],"strong":[88],"correlation":[89],"(":[90],"R":[91],"2":[92],"=":[93],"0.84)":[94],"high":[96],"accuracy":[97],"(mean":[98],"absolute":[99],"error":[100,106],"2.7":[102],"kJ/mol":[103],"root-mean-square":[105],"3.4":[108],"kJ/mol).":[109],"compared":[111],"widely":[115,164],"used":[116,165],"umbrella":[117],"sampling":[118],"(US)":[119],"PaCS-MD":[124],"is":[125,136],"more":[126],"computationally":[127],"efficient":[128],"has":[130],"much":[131],"higher":[132],"accuracy.":[133],"This":[134],"work":[135],"first":[138],"benchmarking":[139],"study":[140,171],"MD":[142],"predicting":[145],"affinities":[148],"uses":[150],"ligands.":[156],"expect":[158],"will":[161,176],"become":[162],"versatile":[167],"tool":[168],"unbinding":[174],"development":[179],"peptides":[181],"applications.":[184]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-06-15T08:34:33.830935","created_date":"2025-12-22T00:00:00"}
