{"id":"https://openalex.org/W4410864091","doi":"https://doi.org/10.1093/bioinformatics/btaf321","title":"Nearl: extracting dynamic features from molecular dynamics trajectories for machine learning tasks","display_name":"Nearl: extracting dynamic features from molecular dynamics trajectories for machine learning tasks","publication_year":2025,"publication_date":"2025-05-29","ids":{"openalex":"https://openalex.org/W4410864091","doi":"https://doi.org/10.1093/bioinformatics/btaf321","pmid":"https://pubmed.ncbi.nlm.nih.gov/40439145"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf321","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf321","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf321/63397357/btaf321.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf321/63397357/btaf321.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101431959","display_name":"Yang Zhang","orcid":"https://orcid.org/0000-0003-0801-8064"},"institutions":[{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Yang Zhang","raw_affiliation_strings":["Department of Biochemistry, University of Zurich , Zurich, 8057,","Department of Biochemistry, University of Zurich, Zurich, 8057, Switzerland"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of Zurich , Zurich, 8057,","institution_ids":["https://openalex.org/I202697423"]},{"raw_affiliation_string":"Department of Biochemistry, University of Zurich, Zurich, 8057, Switzerland","institution_ids":["https://openalex.org/I202697423"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5024363437","display_name":"Andreas Vitalis","orcid":"https://orcid.org/0000-0002-5422-5278"},"institutions":[{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Andreas Vitalis","raw_affiliation_strings":["Department of Biochemistry, University of Zurich , Zurich, 8057,","Department of Biochemistry, University of Zurich, Zurich, 8057, Switzerland"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of Zurich , Zurich, 8057,","institution_ids":["https://openalex.org/I202697423"]},{"raw_affiliation_string":"Department of Biochemistry, University of Zurich, Zurich, 8057, Switzerland","institution_ids":["https://openalex.org/I202697423"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5101431959"],"corresponding_institution_ids":["https://openalex.org/I202697423"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.685,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.83771117,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"41","issue":"7","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":0.9987999796867371,"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":0.9987999796867371,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.9970999956130981,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.9947999715805054,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8445461392402649},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.7017050981521606},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.6159362196922302},{"id":"https://openalex.org/keywords/flexibility","display_name":"Flexibility (engineering)","score":0.5954371690750122},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.5742816925048828},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5630542039871216},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.556280255317688},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.5514687299728394},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.5472164154052734},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5185399651527405},{"id":"https://openalex.org/keywords/personalization","display_name":"Personalization","score":0.4356438219547272},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3968479037284851},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.20316293835639954}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8445461392402649},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7017050981521606},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.6159362196922302},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.5954371690750122},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.5742816925048828},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5630542039871216},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.556280255317688},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.5514687299728394},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.5472164154052734},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5185399651527405},{"id":"https://openalex.org/C183003079","wikidata":"https://www.wikidata.org/wiki/Q1000371","display_name":"Personalization","level":2,"score":0.4356438219547272},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3968479037284851},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.20316293835639954},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","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":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf321","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf321","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf321/63397357/btaf321.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40439145","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40439145","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12233089","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12233089","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf321","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf321","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf321/63397357/btaf321.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","score":0.46000000834465027,"display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G2975229639","display_name":null,"funder_award_id":"189363","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4410864091.pdf","grobid_xml":"https://content.openalex.org/works/W4410864091.grobid-xml"},"referenced_works_count":49,"referenced_works":["https://openalex.org/W2079199763","https://openalex.org/W2079875740","https://openalex.org/W2092285329","https://openalex.org/W2093221728","https://openalex.org/W2169678694","https://openalex.org/W2211722331","https://openalex.org/W2422799170","https://openalex.org/W2529996553","https://openalex.org/W2604320291","https://openalex.org/W2765372792","https://openalex.org/W2781821160","https://openalex.org/W2783073729","https://openalex.org/W2784213390","https://openalex.org/W2892113269","https://openalex.org/W2902812092","https://openalex.org/W2922030663","https://openalex.org/W2990070960","https://openalex.org/W3005364306","https://openalex.org/W3006477052","https://openalex.org/W3019533439","https://openalex.org/W3021453944","https://openalex.org/W3025953134","https://openalex.org/W3042198040","https://openalex.org/W3080540369","https://openalex.org/W3083778208","https://openalex.org/W3083979690","https://openalex.org/W3114024472","https://openalex.org/W3126220825","https://openalex.org/W3168430821","https://openalex.org/W3173197060","https://openalex.org/W3177828909","https://openalex.org/W3186179742","https://openalex.org/W3201695595","https://openalex.org/W3216616254","https://openalex.org/W4233857083","https://openalex.org/W4296032638","https://openalex.org/W4297951436","https://openalex.org/W4382565969","https://openalex.org/W4383186303","https://openalex.org/W4385564481","https://openalex.org/W4386223267","https://openalex.org/W4388638767","https://openalex.org/W4388870515","https://openalex.org/W4392187038","https://openalex.org/W4392928835","https://openalex.org/W4393100309","https://openalex.org/W4396789292","https://openalex.org/W4406241961","https://openalex.org/W4407277076"],"related_works":["https://openalex.org/W2618286804","https://openalex.org/W2329643025","https://openalex.org/W2002770077","https://openalex.org/W3131163342","https://openalex.org/W2092256833","https://openalex.org/W2142369114","https://openalex.org/W2361728394","https://openalex.org/W2166271660","https://openalex.org/W2352631095","https://openalex.org/W3038222916"],"abstract_inverted_index":{"The":[0,13],"source":[1],"code":[2],"of":[3],"Nearl":[4],"is":[5,15],"hosted":[6,16],"at":[7,11,19],"https://github.com/miemiemmmm/Nearl":[8],"and":[9,28],"archived":[10],"https://doi.org/10.5281/zenodo.15320286.":[12],"documentation":[14],"on":[17,30],"ReadTheDocs":[18],"https://nearl.readthedocs.io/en/latest/.":[20],"All":[21],"pre-built":[22],"models":[23],"are":[24],"implemented":[25],"in":[26],"PyTorch":[27],"available":[29],"GitHub.":[31]},"counts_by_year":[{"year":2026,"cited_by_count":2}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
