{"id":"https://openalex.org/W1968378649","doi":"https://doi.org/10.1145/1882291.1882292","title":"Supercomputing in biology","display_name":"Supercomputing in biology","publication_year":2010,"publication_date":"2010-11-07","ids":{"openalex":"https://openalex.org/W1968378649","doi":"https://doi.org/10.1145/1882291.1882292","mag":"1968378649"},"language":"en","primary_location":{"id":"doi:10.1145/1882291.1882292","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1882291.1882292","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the eighteenth ACM SIGSOFT international symposium on Foundations of software engineering","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5024203760","display_name":"Karissa Y. Sanbonmatsu","orcid":"https://orcid.org/0000-0002-7965-7392"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Karissa Y. Sanbonmatsu","raw_affiliation_strings":["Los Alamos National Laboratory, Los Alamos, NM, USA","Los Alamos National Laboratory,Los Alamos, NM, USA"],"affiliations":[{"raw_affiliation_string":"Los Alamos National Laboratory, Los Alamos, NM, USA","institution_ids":["https://openalex.org/I1343871089"]},{"raw_affiliation_string":"Los Alamos National Laboratory,Los Alamos, NM, USA","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5024203760"],"corresponding_institution_ids":["https://openalex.org/I1343871089"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.05462664,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"2"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12029","display_name":"DNA and Biological Computing","score":0.9333999752998352,"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/T12029","display_name":"DNA and Biological Computing","score":0.9333999752998352,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9291999936103821,"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/T11048","display_name":"Bacteriophages and microbial interactions","score":0.901199996471405,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/ribosome","display_name":"Ribosome","score":0.6799825429916382},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.640719473361969},{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.5543622970581055},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.43761155009269714},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4316314458847046},{"id":"https://openalex.org/keywords/translation","display_name":"Translation (biology)","score":0.4220083951950073},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.34649768471717834},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.34381771087646484},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.2801424562931061},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2667439579963684},{"id":"https://openalex.org/keywords/messenger-rna","display_name":"Messenger RNA","score":0.13668560981750488},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12529629468917847}],"concepts":[{"id":"https://openalex.org/C88478588","wikidata":"https://www.wikidata.org/wiki/Q42244","display_name":"Ribosome","level":4,"score":0.6799825429916382},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.640719473361969},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.5543622970581055},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.43761155009269714},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4316314458847046},{"id":"https://openalex.org/C149364088","wikidata":"https://www.wikidata.org/wiki/Q185917","display_name":"Translation (biology)","level":4,"score":0.4220083951950073},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.34649768471717834},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.34381771087646484},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.2801424562931061},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2667439579963684},{"id":"https://openalex.org/C105580179","wikidata":"https://www.wikidata.org/wiki/Q188928","display_name":"Messenger RNA","level":3,"score":0.13668560981750488},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12529629468917847},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/1882291.1882292","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1882291.1882292","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the eighteenth ACM SIGSOFT international symposium on Foundations of software engineering","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2384867379","https://openalex.org/W4400094300","https://openalex.org/W2329539859","https://openalex.org/W2227905990","https://openalex.org/W2765823764","https://openalex.org/W3214280620","https://openalex.org/W3191490922","https://openalex.org/W1582436825","https://openalex.org/W1996803181","https://openalex.org/W2979588510"],"abstract_inverted_index":{"Biotechnology":[0],"has":[1,51],"achieved":[2,36],"exquisite":[3],"control":[4],"over":[5],"many":[6,103],"biological":[7],"systems.":[8],"However,":[9],"to":[10,16,28,55,64,78,114,137,183,198,216,230,242],"design":[11],"drugs":[12],"computationally,":[13],"we":[14,33],"need":[15],"understand":[17],"these":[18,224],"systems":[19],"at":[20],"the":[21,53,71,80,91,106,116,120,129,132,138,141,144,152,159,164,175,186,202,232,244],"atomic":[22,74],"level":[23],"of":[24,48,58,82,85,100,105,140,155,162,174,189,196,211,234,247],"detail":[25],"well":[26],"enough":[27],"predict":[29],"their":[30],"behavior.":[31],"While":[32],"have":[34,178],"not":[35],"this":[37,190],"goal,":[38],"advances":[39],"in":[40,73,88,110,201],"high-performance":[41],"computing":[42,50,182],"are":[43,108,240],"helping":[44],"considerably.":[45],"The":[46],"advent":[47],"petaflop-scale":[49],"opened":[52],"door":[54],"realistic":[56],"simulations":[57,225,239],"biomolecular":[59],"systems,":[60],"making":[61],"it":[62],"possible":[63],"simulate":[65,243],"major":[66],"drug":[67],"targets,":[68],"such":[69],"as":[70],"ribosome,":[72],"detail.":[75],"In":[76,214],"addition":[77,215],"being":[79],"target":[81],"approximately":[83],"half":[84],"antibiotics":[86],"used":[87,179],"US":[89],"hospitals,":[90],"ribosome":[92,107,117,145,203],"is":[93,118],"also":[94],"interesting":[95],"from":[96],"an":[97,227],"evolutionary":[98],"point":[99],"view.":[101],"Because":[102],"regions":[104],"identical":[109],"every":[111,199],"organism":[112],"studied":[113],"date,":[115],"arguably":[119],"oldest":[121],"molecular":[122,191],"fossil,":[123],"and":[124,131,171,204],"represents":[125],"a":[126,147],"bridge":[127],"between":[128],"RNA-world":[130],"modern":[133],"DNA-RNA-protein":[134],"world.":[135],"Analogous":[136],"'CPU":[139],"living":[142],"cell',":[143],"performs":[146],"look-up":[148],"table":[149],"operation,":[150],"converting":[151],"4-letter":[153],"alphabet":[154,161],"genetic":[156],"instructions":[157],"into":[158,185],"20-letter":[160],"proteins,":[163],"cell's":[165],"workhorse":[166],"molecules":[167],"that":[168],"perform":[169],"biochemistry":[170],"constitute":[172],"structures":[173],"cell.":[176],"We":[177],"high":[180],"performance":[181],"delve":[184],"inner":[187],"workings":[188],"factory,":[192],"applying":[193],"Newton's":[194],"equations":[195],"motion":[197],"atom":[200],"its":[205],"surrounding":[206],"environment,":[207],"iterating":[208],"for":[209],"billions":[210],"time":[212],"steps.":[213],"revealing":[217],"mechanistic":[218],"insight":[219],"unattainable":[220],"by":[221],"experimental":[222],"studies,":[223],"present":[226],"excellent":[228],"system":[229],"push":[231],"limits":[233],"supercomputing":[235],"-":[236],"even":[237],"exa-scale":[238],"insufficient":[241],"entire":[245],"process":[246],"protein":[248],"synthesis.":[249]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
