{"id":"https://openalex.org/W2997449405","doi":"https://doi.org/10.1093/bib/bbz149","title":"Computational resources and strategies to assess single-molecule dynamics of the translation process in <i>S. cerevisiae</i>","display_name":"Computational resources and strategies to assess single-molecule dynamics of the translation process in <i>S. cerevisiae</i>","publication_year":2019,"publication_date":"2019-10-31","ids":{"openalex":"https://openalex.org/W2997449405","doi":"https://doi.org/10.1093/bib/bbz149","mag":"2997449405","pmid":"https://pubmed.ncbi.nlm.nih.gov/31879749"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbz149","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbz149","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","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/A5052725708","display_name":"Beatriz T. Magalh\u00e3es","orcid":"https://orcid.org/0000-0003-4434-6989"},"institutions":[{"id":"https://openalex.org/I182534213","display_name":"Universidade do Porto","ror":"https://ror.org/043pwc612","country_code":"PT","type":"education","lineage":["https://openalex.org/I182534213"]}],"countries":["PT"],"is_corresponding":true,"raw_author_name":"Beatriz T Magalh\u00e3es","raw_affiliation_strings":["Faculty of Engineering of the University of Porto, Portugal"],"raw_orcid":"https://orcid.org/0000-0003-4434-6989","affiliations":[{"raw_affiliation_string":"Faculty of Engineering of the University of Porto, Portugal","institution_ids":["https://openalex.org/I182534213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033016354","display_name":"An\u00e1lia Louren\u00e7o","orcid":"https://orcid.org/0000-0001-8401-5362"},"institutions":[{"id":"https://openalex.org/I6289922","display_name":"Universidade de Vigo","ror":"https://ror.org/05rdf8595","country_code":"ES","type":"education","lineage":["https://openalex.org/I6289922"]},{"id":"https://openalex.org/I99682543","display_name":"University of Minho","ror":"https://ror.org/037wpkx04","country_code":"PT","type":"education","lineage":["https://openalex.org/I99682543"]}],"countries":["ES","PT"],"is_corresponding":false,"raw_author_name":"An\u00e1lia Louren\u00e7o","raw_affiliation_strings":["Department of Computer Science, University of Vigo, Spain, Centre of Biological Engineering, University of Minho, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Vigo, Spain, Centre of Biological Engineering, University of Minho, Portugal","institution_ids":["https://openalex.org/I6289922","https://openalex.org/I99682543"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035712663","display_name":"Nuno F. Azevedo","orcid":"https://orcid.org/0000-0001-5864-3250"},"institutions":[{"id":"https://openalex.org/I182534213","display_name":"Universidade do Porto","ror":"https://ror.org/043pwc612","country_code":"PT","type":"education","lineage":["https://openalex.org/I182534213"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Nuno F Azevedo","raw_affiliation_strings":["Department of Chemical Engineering, Faculty of Engineering of the University of Porto, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, Faculty of Engineering of the University of Porto, Portugal","institution_ids":["https://openalex.org/I182534213"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5052725708"],"corresponding_institution_ids":["https://openalex.org/I182534213"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.0859,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.49506972,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"22","issue":"1","first_page":"219","last_page":"231"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9952999949455261,"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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9860000014305115,"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/translation","display_name":"Translation (biology)","score":0.6809351444244385},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.6108658909797668},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5505134463310242},{"id":"https://openalex.org/keywords/dynamics","display_name":"Dynamics (music)","score":0.5171972513198853},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4437692165374756},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3481757640838623},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17671310901641846},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.11680781841278076},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.10397827625274658},{"id":"https://openalex.org/keywords/messenger-rna","display_name":"Messenger RNA","score":0.0836830735206604},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.07922211289405823}],"concepts":[{"id":"https://openalex.org/C149364088","wikidata":"https://www.wikidata.org/wiki/Q185917","display_name":"Translation (biology)","level":4,"score":0.6809351444244385},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.6108658909797668},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5505134463310242},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.5171972513198853},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4437692165374756},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3481757640838623},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17671310901641846},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.11680781841278076},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.10397827625274658},{"id":"https://openalex.org/C105580179","wikidata":"https://www.wikidata.org/wiki/Q188928","display_name":"Messenger RNA","level":3,"score":0.0836830735206604},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07922211289405823},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014176","descriptor_name":"Protein Biosynthesis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014176","descriptor_name":"Protein Biosynthesis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014176","descriptor_name":"Protein Biosynthesis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbz149","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbz149","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31879749","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31879749","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4458402349","display_name":null,"funder_award_id":"ED431C2018/55-GRC","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"}],"funders":[{"id":"https://openalex.org/F4320335322","display_name":"European Regional Development Fund","ror":"https://ror.org/00k4n6c32"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":68,"referenced_works":["https://openalex.org/W830547093","https://openalex.org/W1001283980","https://openalex.org/W1487841058","https://openalex.org/W1799375255","https://openalex.org/W1883779479","https://openalex.org/W1924419326","https://openalex.org/W1924846174","https://openalex.org/W1935289440","https://openalex.org/W1981687980","https://openalex.org/W1984512854","https://openalex.org/W1992927069","https://openalex.org/W1997128348","https://openalex.org/W1997664070","https://openalex.org/W2003560259","https://openalex.org/W2005632880","https://openalex.org/W2011503994","https://openalex.org/W2016542380","https://openalex.org/W2018477176","https://openalex.org/W2022141676","https://openalex.org/W2022209941","https://openalex.org/W2028601571","https://openalex.org/W2029132648","https://openalex.org/W2052360207","https://openalex.org/W2054580373","https://openalex.org/W2059639708","https://openalex.org/W2064569009","https://openalex.org/W2069320301","https://openalex.org/W2073149987","https://openalex.org/W2073711204","https://openalex.org/W2075487771","https://openalex.org/W2078170357","https://openalex.org/W2081545937","https://openalex.org/W2086666821","https://openalex.org/W2088631628","https://openalex.org/W2094179288","https://openalex.org/W2094338137","https://openalex.org/W2096636001","https://openalex.org/W2099102671","https://openalex.org/W2102221598","https://openalex.org/W2117681601","https://openalex.org/W2128149907","https://openalex.org/W2132432514","https://openalex.org/W2140937954","https://openalex.org/W2141803727","https://openalex.org/W2146756673","https://openalex.org/W2149429041","https://openalex.org/W2150704630","https://openalex.org/W2151621038","https://openalex.org/W2153179692","https://openalex.org/W2157613837","https://openalex.org/W2160135160","https://openalex.org/W2162965868","https://openalex.org/W2168387440","https://openalex.org/W2223836536","https://openalex.org/W2285102836","https://openalex.org/W2285122494","https://openalex.org/W2411597730","https://openalex.org/W2499104524","https://openalex.org/W2739047664","https://openalex.org/W2792459789","https://openalex.org/W2803047458","https://openalex.org/W2918941244","https://openalex.org/W3124521395","https://openalex.org/W3136918052","https://openalex.org/W4252039878","https://openalex.org/W6640227043","https://openalex.org/W6670414552","https://openalex.org/W6674632776"],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W4391375266","https://openalex.org/W2078814861","https://openalex.org/W2527526854","https://openalex.org/W1976181487","https://openalex.org/W3167556242"],"abstract_inverted_index":{"This":[0],"work":[1],"provides":[2],"a":[3,141],"systematic":[4],"and":[5,51,56,85,132,143],"comprehensive":[6],"overview":[7],"of":[8,15,32,59,80,111,116,136,138],"available":[9],"resources":[10],"for":[11],"the":[12,16,26,33,45,48,52,63,66,71,83,112,134],"molecular-scale":[13],"modelling":[14,110],"translation":[17,27,113],"process":[18,64,73],"through":[19],"agent-based":[20],"modelling.":[21],"The":[22,37,108],"case":[23],"study":[24],"is":[25,115],"in":[28,62,82,140],"Saccharomyces":[29],"cerevisiae,":[30],"one":[31],"most":[34],"studied":[35],"yeasts.":[36],"data":[38],"curation":[39],"workflow":[40],"encompassed":[41],"structural":[42],"information":[43],"about":[44],"yeast":[46],"(i.e.":[47,65,78,88],"simulation":[49],"environment),":[50],"proteins,":[53],"ribonucleic":[54],"acids":[55],"other":[57],"types":[58],"molecules":[60,81],"involved":[61],"agents).":[67],"Moreover,":[68],"it":[69,121],"covers":[70],"main":[72],"events,":[74],"such":[75,130],"as":[76],"diffusion":[77],"motion":[79],"environment)":[84],"collision":[86],"efficiency":[87],"interaction":[89],"between":[90],"molecules).":[91],"Data":[92],"previously":[93],"determined":[94],"by":[95],"wet-lab":[96],"techniques":[97],"were":[98],"preferred,":[99],"resorting":[100],"to":[101,128],"computational":[102,109],"predictions/extrapolations":[103],"only":[104],"when":[105],"strictly":[106],"necessary.":[107],"processes":[114],"added":[117],"industrial":[118],"interest,":[119],"since":[120],"may":[122],"bring":[123],"forward":[124],"knowledge":[125],"on":[126],"how":[127],"control":[129],"phenomena":[131],"enhance":[133],"production":[135],"proteins":[137],"interest":[139],"faster":[142],"more":[144],"efficient":[145],"manner.":[146]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2020,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2020-01-10T00:00:00"}
