{"id":"https://openalex.org/W4298088990","doi":"https://doi.org/10.1021/acs.jcim.2c00634","title":"Ligand Unbinding Pathway and Mechanism Analysis Assisted by Machine Learning and Graph Methods","display_name":"Ligand Unbinding Pathway and Mechanism Analysis Assisted by Machine Learning and Graph Methods","publication_year":2022,"publication_date":"2022-09-30","ids":{"openalex":"https://openalex.org/W4298088990","doi":"https://doi.org/10.1021/acs.jcim.2c00634","pmid":"https://pubmed.ncbi.nlm.nih.gov/36176219"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.2c00634","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c00634","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/A5027704744","display_name":"Simon Bray","orcid":"https://orcid.org/0000-0002-0621-6705"},"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":false,"raw_author_name":"Simon Bray","raw_affiliation_strings":["Bioinformatics Group, Institute of Informatics, University of Freiburg, 79110Freiburg, Germany","Biomolecular Dynamics, Institute of Physics, University of Freiburg, 79104Freiburg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, Institute of Informatics, University of Freiburg, 79110Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]},{"raw_affiliation_string":"Biomolecular Dynamics, Institute of Physics, University of Freiburg, 79104Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042179929","display_name":"Victor T\u00e4nzel","orcid":"https://orcid.org/0000-0002-1479-1910"},"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":false,"raw_author_name":"Victor T\u00e4nzel","raw_affiliation_strings":["Biomolecular Dynamics, Institute of Physics, University of Freiburg, 79104Freiburg, Germany"],"raw_orcid":"https://orcid.org/0000-0002-1479-1910","affiliations":[{"raw_affiliation_string":"Biomolecular Dynamics, Institute of Physics, University of Freiburg, 79104Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"last","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, 79104Freiburg, Germany"],"raw_orcid":"https://orcid.org/0000-0003-1752-6175","affiliations":[{"raw_affiliation_string":"Biomolecular Dynamics, Institute of Physics, University of Freiburg, 79104Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5080826619"],"corresponding_institution_ids":["https://openalex.org/I161046081"],"apc_list":null,"apc_paid":null,"fwci":1.3887,"has_fulltext":false,"cited_by_count":16,"citation_normalized_percentile":{"value":0.80898044,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"62","issue":"19","first_page":"4591","last_page":"4604"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9995999932289124,"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":0.9995999932289124,"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":0.9991000294685364,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9922999739646912,"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/computer-science","display_name":"Computer science","score":0.657263457775116},{"id":"https://openalex.org/keywords/curse-of-dimensionality","display_name":"Curse of dimensionality","score":0.6470378041267395},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.636829674243927},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.5775747299194336},{"id":"https://openalex.org/keywords/path","display_name":"Path (computing)","score":0.5243996977806091},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4765656292438507},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4510176181793213},{"id":"https://openalex.org/keywords/euclidean-distance","display_name":"Euclidean distance","score":0.4487595856189728},{"id":"https://openalex.org/keywords/hierarchical-clustering","display_name":"Hierarchical clustering","score":0.42712926864624023},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4212486147880554},{"id":"https://openalex.org/keywords/carnivorous-plant","display_name":"Carnivorous plant","score":0.41634654998779297},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.379146933555603},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.32527604699134827},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.15091753005981445}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.657263457775116},{"id":"https://openalex.org/C111030470","wikidata":"https://www.wikidata.org/wiki/Q1430460","display_name":"Curse of dimensionality","level":2,"score":0.6470378041267395},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.636829674243927},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.5775747299194336},{"id":"https://openalex.org/C2777735758","wikidata":"https://www.wikidata.org/wiki/Q817765","display_name":"Path (computing)","level":2,"score":0.5243996977806091},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4765656292438507},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4510176181793213},{"id":"https://openalex.org/C120174047","wikidata":"https://www.wikidata.org/wiki/Q847073","display_name":"Euclidean distance","level":2,"score":0.4487595856189728},{"id":"https://openalex.org/C92835128","wikidata":"https://www.wikidata.org/wiki/Q1277447","display_name":"Hierarchical clustering","level":3,"score":0.42712926864624023},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4212486147880554},{"id":"https://openalex.org/C2777029338","wikidata":"https://www.wikidata.org/wiki/Q18240","display_name":"Carnivorous plant","level":3,"score":0.41634654998779297},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.379146933555603},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.32527604699134827},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.15091753005981445},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C188382862","wikidata":"https://www.wikidata.org/wiki/Q170430","display_name":"Predation","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.2c00634","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c00634","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:36176219","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36176219","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":[],"awards":[{"id":"https://openalex.org/G2558634789","display_name":null,"funder_award_id":"FOR5099 (project No. 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/F4320321990","display_name":"Ministerium f\u00fcr Wissenschaft, Forschung und Kunst Baden-W\u00fcrttemberg","ror":"https://ror.org/01hc18p32"},{"id":"https://openalex.org/F4320334843","display_name":"Freiburg Institute for Advanced Studies, Albert-Ludwigs-Universit\u00e4t Freiburg","ror":"https://ror.org/0245cg223"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":82,"referenced_works":["https://openalex.org/W1031578623","https://openalex.org/W1906064124","https://openalex.org/W1969723894","https://openalex.org/W1969798710","https://openalex.org/W1976499671","https://openalex.org/W1994567486","https://openalex.org/W1996952757","https://openalex.org/W2001357862","https://openalex.org/W2001398410","https://openalex.org/W2011301426","https://openalex.org/W2017196167","https://openalex.org/W2029667189","https://openalex.org/W2035266068","https://openalex.org/W2037535298","https://openalex.org/W2044105167","https://openalex.org/W2045683699","https://openalex.org/W2055298722","https://openalex.org/W2067174909","https://openalex.org/W2072683434","https://openalex.org/W2079385110","https://openalex.org/W2081693079","https://openalex.org/W2085120061","https://openalex.org/W2091392856","https://openalex.org/W2097706568","https://openalex.org/W2099490136","https://openalex.org/W2100152398","https://openalex.org/W2110497788","https://openalex.org/W2128572087","https://openalex.org/W2128686408","https://openalex.org/W2129004089","https://openalex.org/W2140890018","https://openalex.org/W2144288821","https://openalex.org/W2147993766","https://openalex.org/W2149801992","https://openalex.org/W2170711116","https://openalex.org/W2207535250","https://openalex.org/W2216435628","https://openalex.org/W2295598076","https://openalex.org/W2322990480","https://openalex.org/W2334841042","https://openalex.org/W2342249984","https://openalex.org/W2588867992","https://openalex.org/W2606824156","https://openalex.org/W2607348308","https://openalex.org/W2620509108","https://openalex.org/W2767492466","https://openalex.org/W2770164160","https://openalex.org/W2779060209","https://openalex.org/W2794356742","https://openalex.org/W2797820114","https://openalex.org/W2798084948","https://openalex.org/W2801926893","https://openalex.org/W2804603144","https://openalex.org/W2809977614","https://openalex.org/W2888095906","https://openalex.org/W2896638470","https://openalex.org/W2899992883","https://openalex.org/W2940886864","https://openalex.org/W2951182659","https://openalex.org/W2963263006","https://openalex.org/W2987987315","https://openalex.org/W2998547110","https://openalex.org/W2999803602","https://openalex.org/W3003257820","https://openalex.org/W3033513046","https://openalex.org/W3035965352","https://openalex.org/W3099878876","https://openalex.org/W3100923186","https://openalex.org/W3103052184","https://openalex.org/W3112332519","https://openalex.org/W3156234108","https://openalex.org/W3159738363","https://openalex.org/W3160257963","https://openalex.org/W3161090349","https://openalex.org/W4221147630","https://openalex.org/W4224272914","https://openalex.org/W4226055301","https://openalex.org/W4229010429","https://openalex.org/W4254268221","https://openalex.org/W4281643637","https://openalex.org/W4388167314","https://openalex.org/W6697676117"],"related_works":["https://openalex.org/W2487162673","https://openalex.org/W2942366970","https://openalex.org/W2793211469","https://openalex.org/W2949152769","https://openalex.org/W4372354731","https://openalex.org/W2562400057","https://openalex.org/W2577956156","https://openalex.org/W2157179134","https://openalex.org/W2943682648","https://openalex.org/W2390866118"],"abstract_inverted_index":{"We":[0],"present":[1],"two":[2],"methods":[3],"to":[4,61,85],"reveal":[5],"protein-ligand":[6],"unbinding":[7,11,19,44,114],"mechanisms":[8],"in":[9,78,113],"biased":[10],"simulations":[12],"by":[13,41],"clustering":[14],"trajectories":[15,59],"into":[16,73],"ensembles":[17],"representing":[18],"paths.":[20],"The":[21,55],"first":[22],"approach":[23,57],"is":[24,83,103],"based":[25],"on":[26],"a":[27,48,91,104],"contact":[28],"principal":[29],"component":[30],"analysis":[31],"for":[32,52,100],"reducing":[33],"the":[34,37,68,79,96,110],"dimensionality":[35],"of":[36,43],"input":[38,75],"data,":[39],"followed":[40],"identification":[42,102],"paths":[45],"and":[46,82],"training":[47],"machine":[49],"learning":[50],"model":[51],"trajectory":[53],"clustering.":[54],"second":[56],"clusters":[58],"according":[60],"their":[62],"pairwise":[63],"mean":[64],"Euclidean":[65],"distance":[66],"employing":[67],"neighbor-net":[69],"algorithm,":[70],"which":[71],"takes":[72],"account":[74],"data":[76],"bias":[77],"distances":[80],"set":[81],"superior":[84],"dendrogram":[86],"construction.":[87],"Finally,":[88],"we":[89],"describe":[90],"more":[92],"complex":[93],"case":[94],"where":[95],"reaction":[97,116],"coordinate":[98,117],"relevant":[99],"path":[101,115],"single":[105],"intraligand":[106],"hydrogen":[107],"bond,":[108],"highlighting":[109],"challenges":[111],"involved":[112],"detection.":[118]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}