{"id":"https://openalex.org/W4367834949","doi":"https://doi.org/10.1021/acs.jcim.3c00151","title":"Predicting Protein\u2013Ligand Binding and Unbinding Kinetics with Biased MD Simulations and Coarse-Graining of Dynamics: Current State and Challenges","display_name":"Predicting Protein\u2013Ligand Binding and Unbinding Kinetics with Biased MD Simulations and Coarse-Graining of Dynamics: Current State and Challenges","publication_year":2023,"publication_date":"2023-05-03","ids":{"openalex":"https://openalex.org/W4367834949","doi":"https://doi.org/10.1021/acs.jcim.3c00151","pmid":"https://pubmed.ncbi.nlm.nih.gov/37133392"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.3c00151","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c00151","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":"review","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/A5080826619","display_name":"Steffen Wolf","orcid":"https://orcid.org/0000-0003-1752-6175"},"institutions":[{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Steffen Wolf","raw_affiliation_strings":["Biomolecular Dynamics, Institute of Physics, University of Freiburg, 79104 Freiburg, Germany"],"affiliations":[{"raw_affiliation_string":"Biomolecular Dynamics, Institute of Physics, University of Freiburg, 79104 Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5080826619"],"corresponding_institution_ids":["https://openalex.org/I161046081"],"apc_list":null,"apc_paid":null,"fwci":5.7587,"has_fulltext":false,"cited_by_count":37,"citation_normalized_percentile":{"value":0.96666444,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"63","issue":"10","first_page":"2902","last_page":"2910"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9994999766349792,"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/T11178","display_name":"Receptor Mechanisms and Signaling","score":0.9932000041007996,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/kinetics","display_name":"Kinetics","score":0.7592000961303711},{"id":"https://openalex.org/keywords/granularity","display_name":"Granularity","score":0.7559107542037964},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.7378957271575928},{"id":"https://openalex.org/keywords/receptor\u2013ligand-kinetics","display_name":"Receptor\u2013ligand kinetics","score":0.6314136385917664},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.5473856329917908},{"id":"https://openalex.org/keywords/current","display_name":"Current (fluid)","score":0.5033039450645447},{"id":"https://openalex.org/keywords/dynamics","display_name":"Dynamics (music)","score":0.4916868805885315},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.4235490560531616},{"id":"https://openalex.org/keywords/chemical-physics","display_name":"Chemical physics","score":0.33094531297683716},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.2905043959617615},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.28272736072540283},{"id":"https://openalex.org/keywords/thermodynamics","display_name":"Thermodynamics","score":0.243413507938385},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.22705715894699097},{"id":"https://openalex.org/keywords/classical-mechanics","display_name":"Classical mechanics","score":0.103078693151474}],"concepts":[{"id":"https://openalex.org/C148898269","wikidata":"https://www.wikidata.org/wiki/Q1108792","display_name":"Kinetics","level":2,"score":0.7592000961303711},{"id":"https://openalex.org/C177774035","wikidata":"https://www.wikidata.org/wiki/Q1246948","display_name":"Granularity","level":2,"score":0.7559107542037964},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.7378957271575928},{"id":"https://openalex.org/C152900378","wikidata":"https://www.wikidata.org/wiki/Q7302366","display_name":"Receptor\u2013ligand kinetics","level":3,"score":0.6314136385917664},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.5473856329917908},{"id":"https://openalex.org/C148043351","wikidata":"https://www.wikidata.org/wiki/Q4456944","display_name":"Current (fluid)","level":2,"score":0.5033039450645447},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.4916868805885315},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4235490560531616},{"id":"https://openalex.org/C159467904","wikidata":"https://www.wikidata.org/wiki/Q2001702","display_name":"Chemical physics","level":1,"score":0.33094531297683716},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.2905043959617615},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.28272736072540283},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.243413507938385},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.22705715894699097},{"id":"https://openalex.org/C74650414","wikidata":"https://www.wikidata.org/wiki/Q11397","display_name":"Classical mechanics","level":1,"score":0.103078693151474},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0}],"mesh":[{"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":"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":"D010825","descriptor_name":"Physics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010825","descriptor_name":"Physics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010825","descriptor_name":"Physics","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":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":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.3c00151","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c00151","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:37133392","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37133392","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":0.8299999833106995,"id":"https://metadata.un.org/sdg/7"}],"awards":[{"id":"https://openalex.org/G2352271043","display_name":null,"funder_award_id":"431945604","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G565477956","display_name":null,"funder_award_id":"WO 2410/2-1","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G8791088295","display_name":null,"funder_award_id":"INST 37/935-1 FUGG","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320321112","display_name":"Eberhard Karls Universit\u00e4t T\u00fcbingen","ror":"https://ror.org/03a1kwz48"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":101,"referenced_works":["https://openalex.org/W185137928","https://openalex.org/W1230652463","https://openalex.org/W1906064124","https://openalex.org/W1952317074","https://openalex.org/W1969723894","https://openalex.org/W1975310895","https://openalex.org/W1997231673","https://openalex.org/W2001357862","https://openalex.org/W2014952106","https://openalex.org/W2016408686","https://openalex.org/W2019877102","https://openalex.org/W2028245191","https://openalex.org/W2034139972","https://openalex.org/W2040370739","https://openalex.org/W2049617698","https://openalex.org/W2059008956","https://openalex.org/W2063945425","https://openalex.org/W2065907078","https://openalex.org/W2072456220","https://openalex.org/W2083551083","https://openalex.org/W2085266415","https://openalex.org/W2086673864","https://openalex.org/W2099490136","https://openalex.org/W2099598754","https://openalex.org/W2110497788","https://openalex.org/W2114621223","https://openalex.org/W2133620840","https://openalex.org/W2135732933","https://openalex.org/W2149042430","https://openalex.org/W2149801992","https://openalex.org/W2171047927","https://openalex.org/W2207535250","https://openalex.org/W2346590986","https://openalex.org/W2369974116","https://openalex.org/W2397367200","https://openalex.org/W2439566903","https://openalex.org/W2554932040","https://openalex.org/W2588867992","https://openalex.org/W2607348308","https://openalex.org/W2623055862","https://openalex.org/W2742127985","https://openalex.org/W2767492466","https://openalex.org/W2775730699","https://openalex.org/W2779060209","https://openalex.org/W2794356742","https://openalex.org/W2801926893","https://openalex.org/W2804603144","https://openalex.org/W2888095906","https://openalex.org/W2889287654","https://openalex.org/W2896638470","https://openalex.org/W2899992883","https://openalex.org/W2902663544","https://openalex.org/W2904535843","https://openalex.org/W2917833092","https://openalex.org/W2924677843","https://openalex.org/W2940886864","https://openalex.org/W2945543304","https://openalex.org/W2949752042","https://openalex.org/W2963263006","https://openalex.org/W2967780898","https://openalex.org/W2987987315","https://openalex.org/W2999469162","https://openalex.org/W2999803602","https://openalex.org/W3008279928","https://openalex.org/W3035815479","https://openalex.org/W3037317174","https://openalex.org/W3043528025","https://openalex.org/W3044187902","https://openalex.org/W3044938537","https://openalex.org/W3054319032","https://openalex.org/W3087357377","https://openalex.org/W3089247149","https://openalex.org/W3090513030","https://openalex.org/W3100923186","https://openalex.org/W3121332380","https://openalex.org/W3156234108","https://openalex.org/W3161090349","https://openalex.org/W3180124170","https://openalex.org/W3198320390","https://openalex.org/W3209739359","https://openalex.org/W4200067775","https://openalex.org/W4210275019","https://openalex.org/W4210676315","https://openalex.org/W4224272914","https://openalex.org/W4225585143","https://openalex.org/W4226055301","https://openalex.org/W4285744851","https://openalex.org/W4293498983","https://openalex.org/W4296162938","https://openalex.org/W4296897111","https://openalex.org/W4296954235","https://openalex.org/W4298088990","https://openalex.org/W4298125158","https://openalex.org/W4308635391","https://openalex.org/W4312140457","https://openalex.org/W4353031804","https://openalex.org/W4353109120","https://openalex.org/W4361206180","https://openalex.org/W4361295032","https://openalex.org/W4362608511","https://openalex.org/W4388167314"],"related_works":["https://openalex.org/W2002491498","https://openalex.org/W1850634138","https://openalex.org/W1980203814","https://openalex.org/W2044634375","https://openalex.org/W2035059921","https://openalex.org/W1974796988","https://openalex.org/W2187012192","https://openalex.org/W39860180","https://openalex.org/W2063702932","https://openalex.org/W2724766721"],"abstract_inverted_index":{"The":[0],"prediction":[1],"of":[2,34,41,47,61,66],"drug-target":[3],"binding":[4,54,73],"and":[5,15,37,55],"unbinding":[6,56],"kinetics":[7,57,68],"that":[8],"occur":[9],"on":[10],"time":[11],"scales":[12],"between":[13],"milliseconds":[14],"several":[16],"hours":[17],"is":[18],"a":[19,31],"prime":[20],"challenge":[21],"for":[22],"biased":[23,45],"molecular":[24,51],"dynamics":[25],"simulation":[26],"approaches.":[27],"This":[28],"Perspective":[29],"gives":[30],"concise":[32],"summary":[33],"the":[35,38,50,62],"theory":[36],"current":[39],"state-of-the-art":[40],"such":[42],"predictions":[43,65],"via":[44],"simulations,":[46],"insights":[48],"into":[49],"mechanisms":[52],"defining":[53],"as":[58,60],"well":[59],"extraordinary":[63],"challenges":[64],"ligand":[67],"pose":[69],"in":[70],"comparison":[71],"to":[72],"free":[74],"energy":[75],"predictions.":[76]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":11},{"year":2024,"cited_by_count":12},{"year":2023,"cited_by_count":11}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}