{"id":"https://openalex.org/W7220943000","doi":"https://doi.org/10.64898/2026.10.07.757317","title":"Exploration of ligand (un)binding trajectories with Rosetta","display_name":"Exploration of ligand (un)binding trajectories with Rosetta","publication_year":2026,"publication_date":"2026-10-08","ids":{"openalex":"https://openalex.org/W7220943000","doi":"https://doi.org/10.64898/2026.10.07.757317"},"language":"en","primary_location":{"id":"doi:10.64898/2026.10.07.757317","doi":"https://doi.org/10.64898/2026.10.07.757317","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.07.757317","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/08/2026.10.07.757317.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/08/2026.10.07.757317.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5079517265","display_name":"Alexander S. Zlobin","orcid":"https://orcid.org/0000-0001-8627-0455","observed_orcids":["https://orcid.org/0000-0001-8627-0455"]},"institutions":[{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Alexander Zlobin","raw_affiliation_strings":["Institute for Drug Discovery, Leipzig University, 04103, Leipzig, Germany","Interdisciplinary Center for Bioinformatics, Leipzig University, 04107 Leipzig, Germany"],"raw_orcid":"https://orcid.org/0000-0001-8627-0455","affiliations":[{"raw_affiliation_string":"Institute for Drug Discovery, Leipzig University, 04103, Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]},{"raw_affiliation_string":"Interdisciplinary Center for Bioinformatics, Leipzig University, 04107 Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5095941677","display_name":"Paul Eisenhuth","orcid":"https://orcid.org/0009-0006-7379-5096","observed_orcids":["https://orcid.org/0009-0006-7379-5096"]},"institutions":[{"id":"https://openalex.org/I4401726909","display_name":"Center for Scalable Data Analytics and Artificial Intelligence","ror":"https://ror.org/01t4ttr56","country_code":"DE","type":"education","lineage":["https://openalex.org/I4401726909","https://openalex.org/I78650965","https://openalex.org/I926574661"]},{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Paul Eisenhuth","raw_affiliation_strings":["Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI) Dresden/Leipzig, Leipzig University, 04105, Leipzig, Germany","Institute for Drug Discovery, Leipzig University, 04103, Leipzig, Germany"],"raw_orcid":"https://orcid.org/0009-0006-7379-5096","affiliations":[{"raw_affiliation_string":"Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI) Dresden/Leipzig, Leipzig University, 04105, Leipzig, Germany","institution_ids":["https://openalex.org/I4401726909","https://openalex.org/I926574661"]},{"raw_affiliation_string":"Institute for Drug Discovery, Leipzig University, 04103, Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103027251","display_name":"Valerio Ferrario","orcid":"https://orcid.org/0000-0002-4233-4805","observed_orcids":["https://orcid.org/0000-0002-4233-4805"]},"institutions":[{"id":"https://openalex.org/I4210107087","display_name":"BASF (Germany)","ror":"https://ror.org/01q8f6705","country_code":"DE","type":"company","lineage":["https://openalex.org/I4210107087"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Valerio Ferrario","raw_affiliation_strings":["BASF SE, 67056 Ludwigshafen am Rhein, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BASF SE, 67056 Ludwigshafen am Rhein, Germany","institution_ids":["https://openalex.org/I4210107087"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025842562","display_name":"Jens Meiler","orcid":"https://orcid.org/0000-0001-8945-193X","observed_orcids":["https://orcid.org/0000-0001-8945-193X"]},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]},{"id":"https://openalex.org/I4401726909","display_name":"Center for Scalable Data Analytics and Artificial Intelligence","ror":"https://ror.org/01t4ttr56","country_code":"DE","type":"education","lineage":["https://openalex.org/I4401726909","https://openalex.org/I78650965","https://openalex.org/I926574661"]},{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["DE","US"],"is_corresponding":false,"raw_author_name":"Jens Meiler","raw_affiliation_strings":["Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI) Dresden/Leipzig, Leipzig University, 04105, Leipzig, Germany","Center for Structural Biology, Vanderbilt University, Nashville, TN, 37235, USA","Department of Chemistry, Department of Pharmacology and Institute of Chemical Biology, Vanderbilt University, Nashville, TN, 37235, USA","Institute for Drug Discovery, Leipzig University, 04103, Leipzig, Germany","School of Embedded Composite Artificial Intelligence SECAI, 04105, Leipzig, Germany"],"raw_orcid":"https://orcid.org/0000-0001-8945-193X","affiliations":[{"raw_affiliation_string":"Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI) Dresden/Leipzig, Leipzig University, 04105, Leipzig, Germany","institution_ids":["https://openalex.org/I4401726909","https://openalex.org/I926574661"]},{"raw_affiliation_string":"Center for Structural Biology, Vanderbilt University, Nashville, TN, 37235, USA","institution_ids":["https://openalex.org/I200719446"]},{"raw_affiliation_string":"Department of Chemistry, Department of Pharmacology and Institute of Chemical Biology, Vanderbilt University, Nashville, TN, 37235, USA","institution_ids":["https://openalex.org/I200719446"]},{"raw_affiliation_string":"Institute for Drug Discovery, Leipzig University, 04103, Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]},{"raw_affiliation_string":"School of Embedded Composite Artificial Intelligence SECAI, 04105, Leipzig, Germany","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5079517265"],"corresponding_institution_ids":["https://openalex.org/I926574661"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"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":0.9829000234603882,"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":0.9829000234603882,"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":0.01489999983459711,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.0006000000284984708,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural 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/ligand-transport","display_name":"ligand transport","score":0.734000027179718},{"id":"https://openalex.org/keywords/protein-ligand-binding","display_name":"protein-ligand binding","score":0.7580000162124634},{"id":"https://openalex.org/keywords/protein-flexibility","display_name":"protein flexibility","score":0.7990000247955322},{"id":"https://openalex.org/keywords/enzyme-design","display_name":"enzyme design","score":0.6729999780654907},{"id":"https://openalex.org/keywords/molecular-dynamics-simulation","display_name":"molecular dynamics simulation","score":0.6150000095367432},{"id":"https://openalex.org/keywords/ligand-binding-prediction","display_name":"ligand binding prediction","score":0.33500000834465027}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6040999889373779},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.580299973487854},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.45170000195503235},{"id":"https://openalex.org/C2778012447","wikidata":"https://www.wikidata.org/wiki/Q1034415","display_name":"Scope (computer science)","level":2,"score":0.44609999656677246},{"id":"https://openalex.org/C177606310","wikidata":"https://www.wikidata.org/wiki/Q5674297","display_name":"Adaptability","level":2,"score":0.40700000524520874},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.3637999892234802},{"id":"https://openalex.org/C176147130","wikidata":"https://www.wikidata.org/wiki/Q909622","display_name":"Evolvability","level":2,"score":0.3359000086784363},{"id":"https://openalex.org/C106131492","wikidata":"https://www.wikidata.org/wiki/Q3072260","display_name":"Filter (signal processing)","level":2,"score":0.3352999985218048},{"id":"https://openalex.org/C152769699","wikidata":"https://www.wikidata.org/wiki/Q410814","display_name":"Protein design","level":3,"score":0.32510000467300415},{"id":"https://openalex.org/C109095088","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Protein ligand","level":2,"score":0.3061000108718872},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.30300000309944153},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.29820001125335693},{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.26820001006126404},{"id":"https://openalex.org/C2776184637","wikidata":"https://www.wikidata.org/wiki/Q6506039","display_name":"Living systems","level":2,"score":0.26750001311302185},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.25920000672340393},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.250900000333786},{"id":"https://openalex.org/C2777936996","wikidata":"https://www.wikidata.org/wiki/Q17148461","display_name":"Conformational ensembles","level":3,"score":0.25049999356269836},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2500999867916107}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.10.07.757317","doi":"https://doi.org/10.64898/2026.10.07.757317","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.07.757317","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/08/2026.10.07.757317.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.10.07.757317","doi":"https://doi.org/10.64898/2026.10.07.757317","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.07.757317","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/08/2026.10.07.757317.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"},{"id":"https://openalex.org/F4320330124","display_name":"German Network for Bioinformatics Infrastructure","ror":"https://ror.org/01vmpm840"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7220943000.pdf","grobid_xml":"https://content.openalex.org/works/W7220943000.grobid-xml"},"referenced_works_count":4,"referenced_works":["https://openalex.org/W2955632566","https://openalex.org/W3154034682","https://openalex.org/W3203566188","https://openalex.org/W4413950864"],"related_works":["https://openalex.org/W2127803531","https://openalex.org/W2588940733","https://openalex.org/W2944202352","https://openalex.org/W1999008973","https://openalex.org/W4283209409","https://openalex.org/W2600773364","https://openalex.org/W3043252841","https://openalex.org/W2901083920","https://openalex.org/W2146097585","https://openalex.org/W2955632566"],"abstract_inverted_index":{"Abstract":[0],"Ligand":[1],"transport":[2,125],"through":[3],"proteins":[4],"underlies":[5],"many":[6],"aspects":[7],"of":[8,39,80,90,114,152,162,168],"molecular":[9],"function,":[10],"but":[11,28,49],"its":[12,131],"detailed":[13],"mechanisms":[14],"remain":[15],"largely":[16],"inaccessible":[17],"to":[18,60,76,118,133,159,164],"direct":[19],"observation.":[20],"Molecular":[21],"dynamics":[22,167],"simulations":[23],"could":[24],"close":[25],"this":[26],"gap,":[27],"are":[29],"computationally":[30],"too":[31],"demanding":[32],"for":[33,54,110],"practical":[34,72],"purposes,":[35],"including":[36],"filtering":[37],"stages":[38],"enzyme":[40,144],"design":[41,145],"pipelines.":[42],"Simplified":[43],"docking-based":[44],"approaches":[45],"might":[46,58],"be":[47],"informative,":[48],"sometimes":[50],"the":[51,81,160,166],"oversimplifications":[52],"required":[53],"high":[55],"throughput":[56],"applications":[57],"lead":[59],"unreliable":[61],"predictions.":[62],"Here":[63],"we":[64],"present":[65],"RosettaLigand":[66],"PathFinder":[67],"(RLPF),":[68],"a":[69,95,111,141,156],"fast":[70],"and":[71,85,88,108,127,138,149,173],"tool":[73],"explicitly":[74],"built":[75],"ensure":[77],"conformational":[78],"continuity":[79],"ligand":[82,86],"trajectory,":[83],"protein":[84],"flexibility,":[87],"robustness":[89],"every":[91],"run.":[92],"Built":[93],"using":[94],"flexible":[96],"RosettaScripts":[97],"XML":[98],"interface,":[99],"it":[100,155],"enables":[101],"fine-grained":[102],"control":[103],"over":[104],"all":[105],"simulation":[106],"parameters":[107],"adaptability":[109],"wide":[112],"range":[113],"use":[115],"cases.":[116],"Applied":[117],"several":[119],"representative":[120],"systems,":[121],"RLPF":[122,153],"reproduced":[123],"established":[124],"features":[126],"mutation":[128],"effects,":[129],"highlighting":[130],"ability":[132],"produce":[134],"biologically":[135],"relevant":[136],"insights":[137],"serve":[139],"as":[140],"filter":[142],"in":[143],"campaigns.":[146],"Wide":[147],"customizability":[148],"well-defined":[150],"scope":[151],"make":[154],"useful":[157],"addition":[158],"family":[161],"tools":[163],"study":[165],"interactions":[169],"between":[170],"small":[171],"molecules":[172],"proteins.":[174]},"counts_by_year":[],"updated_date":"2026-11-08T12:12:28.789561","created_date":"2026-10-09T00:00:00"}
