{"id":"https://openalex.org/W2292169708","doi":"https://doi.org/10.1093/bioinformatics/btw020","title":"SIRAH tools: mapping, backmapping and visualization of coarse-grained models","display_name":"SIRAH tools: mapping, backmapping and visualization of coarse-grained models","publication_year":2016,"publication_date":"2016-01-14","ids":{"openalex":"https://openalex.org/W2292169708","doi":"https://doi.org/10.1093/bioinformatics/btw020","mag":"2292169708"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw020","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw020","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"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/A5005916377","display_name":"Mat\u00edas Machado","orcid":"https://orcid.org/0000-0002-9971-4710"},"institutions":[{"id":"https://openalex.org/I4210156231","display_name":"Institut Pasteur de Montevideo","ror":"https://ror.org/04dpm2z73","country_code":"UY","type":"facility","lineage":["https://openalex.org/I4210156231"]}],"countries":["UY"],"is_corresponding":true,"raw_author_name":"Mat\u00edas R. Machado","raw_affiliation_strings":["Biomolecular Simulations, Institut Pasteur De Montevideo, Montevideo 11400, Uruguay"],"affiliations":[{"raw_affiliation_string":"Biomolecular Simulations, Institut Pasteur De Montevideo, Montevideo 11400, Uruguay","institution_ids":["https://openalex.org/I4210156231"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035123082","display_name":"Sergio Pantano","orcid":"https://orcid.org/0000-0001-6435-4543"},"institutions":[{"id":"https://openalex.org/I4210156231","display_name":"Institut Pasteur de Montevideo","ror":"https://ror.org/04dpm2z73","country_code":"UY","type":"facility","lineage":["https://openalex.org/I4210156231"]}],"countries":["UY"],"is_corresponding":true,"raw_author_name":"Sergio Pantano","raw_affiliation_strings":["Biomolecular Simulations, Institut Pasteur De Montevideo, Montevideo 11400, Uruguay"],"affiliations":[{"raw_affiliation_string":"Biomolecular Simulations, Institut Pasteur De Montevideo, Montevideo 11400, Uruguay","institution_ids":["https://openalex.org/I4210156231"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5005916377","https://openalex.org/A5035123082"],"corresponding_institution_ids":["https://openalex.org/I4210156231"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":7.1468,"has_fulltext":false,"cited_by_count":135,"citation_normalized_percentile":{"value":0.97470811,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"32","issue":"10","first_page":"1568","last_page":"1570"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9991999864578247,"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":0.9991999864578247,"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":0.9979000091552734,"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/T11809","display_name":"Advanced NMR Techniques and Applications","score":0.9976000189781189,"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":0.7942925691604614},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.7654005885124207},{"id":"https://openalex.org/keywords/perl","display_name":"Perl","score":0.7050718069076538},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.6720757484436035},{"id":"https://openalex.org/keywords/plug-in","display_name":"Plug-in","score":0.6450663805007935},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.49635201692581177},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.4582291543483734},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.4566967785358429},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.44872939586639404},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.43840548396110535},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3643326163291931},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3310731053352356},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2913416624069214}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7942925691604614},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.7654005885124207},{"id":"https://openalex.org/C2777002779","wikidata":"https://www.wikidata.org/wiki/Q42478","display_name":"Perl","level":2,"score":0.7050718069076538},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.6720757484436035},{"id":"https://openalex.org/C4924752","wikidata":"https://www.wikidata.org/wiki/Q184148","display_name":"Plug-in","level":2,"score":0.6450663805007935},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.49635201692581177},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.4582291543483734},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.4566967785358429},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.44872939586639404},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.43840548396110535},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3643326163291931},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3310731053352356},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2913416624069214},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btw020","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw020","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:HAL:pasteur-01498356v1","is_oa":false,"landing_page_url":"https://riip.hal.science/pasteur-01498356","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, 2016, 32 (10), pp.1568-70. &#x27E8;10.1093/bioinformatics/btw020&#x27E9;","raw_type":"Journal articles"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:32/10/1568","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/10/1568","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":12,"referenced_works":["https://openalex.org/W1806547840","https://openalex.org/W2029667189","https://openalex.org/W2085943043","https://openalex.org/W2103325328","https://openalex.org/W2104078482","https://openalex.org/W2132262459","https://openalex.org/W2141920771","https://openalex.org/W2154714625","https://openalex.org/W2160544821","https://openalex.org/W2319900881","https://openalex.org/W2331280184","https://openalex.org/W2416757576"],"related_works":["https://openalex.org/W2412623563","https://openalex.org/W190299232","https://openalex.org/W1521481095","https://openalex.org/W594361471","https://openalex.org/W2604964690","https://openalex.org/W2417897055","https://openalex.org/W66419302","https://openalex.org/W207660752","https://openalex.org/W3121352828","https://openalex.org/W1486009489"],"abstract_inverted_index":{"Abstract":[0],"Summary:":[1],"Coarse-grained":[2],"(CG)":[3],"models":[4],"reduce":[5],"the":[6,13,19,29,78,85,93],"cost":[7],"of":[8,15,21,33,41,87,102],"molecular":[9,16],"dynamics":[10],"simulations":[11],"keeping":[12],"essence":[14],"interactions.":[17],"Still,":[18],"diversity":[20],"CG":[22,50,74,89],"representations":[23],"(sizes,":[24],"connectivity,":[25],"naming,":[26],"etc.)":[27],"hampers":[28],"handling":[30],"and":[31,62,69,98,113],"visualization":[32],"such":[34],"models.":[35],"SIRAH":[36,79,103],"Tools":[37,104],"comprises":[38],"a":[39,63],"set":[40],"utilities":[42,101],"to":[43,47,66],"convert":[44],"all-atoms":[45],"coordinates":[46],"arbitrary":[48],"residue-based":[49],"schemes,":[51],"write":[52],"GROMACS\u2019":[53],"topological":[54],"information":[55,72],"at":[56,119],"any":[57],"resolution":[58],"into":[59],"PSF":[60],"format":[61],"VMD":[64],"plugin":[65],"visualize,":[67],"analyze":[68],"retrieve":[70],"pseudo-atomistic":[71],"from":[73],"trajectories":[75],"performed":[76],"with":[77],"force":[80,90],"field.":[81],"These":[82],"tools":[83],"facilitate":[84],"use":[86],"intricate":[88],"fields":[91],"outside":[92],"small":[94],"developer\u2019s":[95],"community.":[96],"Availability":[97],"implementation:":[99],"Different":[100],"are":[105,116],"written":[106],"in":[107],"Perl,":[108],"Tcl,":[109],"or":[110,123],"R.":[111],"Documentation":[112],"source":[114],"codes":[115],"freely":[117],"distributed":[118],"http://www.sirahff.com.":[120],"Contact:":[121],"mmachado@pasteur.edu.uy":[122],"spantano@pasteur.edu.uy":[124]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":15},{"year":2024,"cited_by_count":17},{"year":2023,"cited_by_count":15},{"year":2022,"cited_by_count":12},{"year":2021,"cited_by_count":17},{"year":2020,"cited_by_count":15},{"year":2019,"cited_by_count":18},{"year":2018,"cited_by_count":9},{"year":2017,"cited_by_count":9},{"year":2016,"cited_by_count":5}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2016-06-24T00:00:00"}
