{"id":"https://openalex.org/W2557647417","doi":"https://doi.org/10.1145/2975167.2975199","title":"OCoM-SOCoM","display_name":"OCoM-SOCoM","publication_year":2016,"publication_date":"2016-10-02","ids":{"openalex":"https://openalex.org/W2557647417","doi":"https://doi.org/10.1145/2975167.2975199","mag":"2557647417"},"language":"en","primary_location":{"id":"doi:10.1145/2975167.2975199","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2975167.2975199","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","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/A5062942017","display_name":"Deeptak Verma","orcid":"https://orcid.org/0000-0003-0740-0624"},"institutions":[{"id":"https://openalex.org/I107672454","display_name":"Dartmouth College","ror":"https://ror.org/049s0rh22","country_code":"US","type":"education","lineage":["https://openalex.org/I107672454"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Deeptak Verma","raw_affiliation_strings":["Dept. of Computer Science, Dartmouth College, Hanover, New Hampshire, USA"],"affiliations":[{"raw_affiliation_string":"Dept. of Computer Science, Dartmouth College, Hanover, New Hampshire, USA","institution_ids":["https://openalex.org/I107672454"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031865026","display_name":"Gevorg Grigoryan","orcid":"https://orcid.org/0000-0003-4645-7666"},"institutions":[{"id":"https://openalex.org/I107672454","display_name":"Dartmouth College","ror":"https://ror.org/049s0rh22","country_code":"US","type":"education","lineage":["https://openalex.org/I107672454"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gevorg Grigoryan","raw_affiliation_strings":["Dept. of Computer Science, Dept. of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA"],"affiliations":[{"raw_affiliation_string":"Dept. of Computer Science, Dept. of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA","institution_ids":["https://openalex.org/I107672454"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5030579910","display_name":"Chris Bailey\u2010Kellogg","orcid":"https://orcid.org/0000-0003-1860-0912"},"institutions":[{"id":"https://openalex.org/I107672454","display_name":"Dartmouth College","ror":"https://ror.org/049s0rh22","country_code":"US","type":"education","lineage":["https://openalex.org/I107672454"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chris Bailey-Kellogg","raw_affiliation_strings":["Dept. of Computer Science, Dartmouth College, Hanover, New Hampshire, USA"],"affiliations":[{"raw_affiliation_string":"Dept. of Computer Science, Dartmouth College, Hanover, New Hampshire, USA","institution_ids":["https://openalex.org/I107672454"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5062942017"],"corresponding_institution_ids":["https://openalex.org/I107672454"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.09625192,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"307","last_page":"316"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9955000281333923,"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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9955000281333923,"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":0.9941999912261963,"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":0.993399977684021,"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/computer-science","display_name":"Computer science","score":0.6212826371192932},{"id":"https://openalex.org/keywords/protein-design","display_name":"Protein design","score":0.5374636650085449},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5200098156929016},{"id":"https://openalex.org/keywords/mutagenesis","display_name":"Mutagenesis","score":0.5090072154998779},{"id":"https://openalex.org/keywords/pareto-principle","display_name":"Pareto principle","score":0.508539080619812},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4970395863056183},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.41864120960235596},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.40703830122947693},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3256677985191345},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.2796964645385742},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.25324124097824097},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2532021999359131},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.2529529333114624},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.19705620408058167},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.15725621581077576},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.14754483103752136},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.11029589176177979}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6212826371192932},{"id":"https://openalex.org/C152769699","wikidata":"https://www.wikidata.org/wiki/Q410814","display_name":"Protein design","level":3,"score":0.5374636650085449},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5200098156929016},{"id":"https://openalex.org/C16318435","wikidata":"https://www.wikidata.org/wiki/Q149299","display_name":"Mutagenesis","level":4,"score":0.5090072154998779},{"id":"https://openalex.org/C137635306","wikidata":"https://www.wikidata.org/wiki/Q182667","display_name":"Pareto principle","level":2,"score":0.508539080619812},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4970395863056183},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.41864120960235596},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.40703830122947693},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3256677985191345},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.2796964645385742},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.25324124097824097},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2532021999359131},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.2529529333114624},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.19705620408058167},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.15725621581077576},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.14754483103752136},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.11029589176177979},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/2975167.2975199","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2975167.2975199","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","score":0.5799999833106995,"display_name":"Affordable and clean energy"}],"awards":[{"id":"https://openalex.org/G2642809447","display_name":null,"funder_award_id":"R01-GM-098977","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320310400","display_name":"Dartmouth College","ror":"https://ror.org/049s0rh22"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":60,"referenced_works":["https://openalex.org/W160919370","https://openalex.org/W1548178570","https://openalex.org/W1599677668","https://openalex.org/W1730919420","https://openalex.org/W1905590028","https://openalex.org/W1965315112","https://openalex.org/W1967514651","https://openalex.org/W1992082328","https://openalex.org/W1998581507","https://openalex.org/W2007337775","https://openalex.org/W2007685030","https://openalex.org/W2008545402","https://openalex.org/W2009123297","https://openalex.org/W2010964231","https://openalex.org/W2013412105","https://openalex.org/W2014323977","https://openalex.org/W2020898082","https://openalex.org/W2022871424","https://openalex.org/W2026219411","https://openalex.org/W2030695915","https://openalex.org/W2035997808","https://openalex.org/W2036742051","https://openalex.org/W2037212291","https://openalex.org/W2049695588","https://openalex.org/W2051363480","https://openalex.org/W2051687036","https://openalex.org/W2054621971","https://openalex.org/W2072901888","https://openalex.org/W2083414265","https://openalex.org/W2084262300","https://openalex.org/W2089615190","https://openalex.org/W2089710023","https://openalex.org/W2094392347","https://openalex.org/W2101721207","https://openalex.org/W2106775540","https://openalex.org/W2114357419","https://openalex.org/W2114869075","https://openalex.org/W2115202121","https://openalex.org/W2121489857","https://openalex.org/W2127068865","https://openalex.org/W2129450171","https://openalex.org/W2131447885","https://openalex.org/W2133844804","https://openalex.org/W2135237787","https://openalex.org/W2136319352","https://openalex.org/W2139413955","https://openalex.org/W2153965985","https://openalex.org/W2154543415","https://openalex.org/W2155095892","https://openalex.org/W2161792971","https://openalex.org/W2166475106","https://openalex.org/W2168142063","https://openalex.org/W2169805130","https://openalex.org/W2170174589","https://openalex.org/W2171002584","https://openalex.org/W2171224768","https://openalex.org/W2360686623","https://openalex.org/W2415038042","https://openalex.org/W2903758591","https://openalex.org/W4252751859"],"related_works":["https://openalex.org/W2378211422","https://openalex.org/W4321353415","https://openalex.org/W2745001401","https://openalex.org/W2130974462","https://openalex.org/W2028665553","https://openalex.org/W2086519370","https://openalex.org/W972276598","https://openalex.org/W2087343574","https://openalex.org/W4246352526","https://openalex.org/W2121910908"],"abstract_inverted_index":{"High-throughput":[0],"screening":[1],"of":[2,12,28,32,76,88,113,119],"combinatorial":[3,62],"mutagenesis":[4],"libraries":[5,63,139,173],"has":[6],"enabled":[7],"and":[8,71,156,169,186],"accelerated":[9],"the":[10,19,29,67,72,86,117],"development":[11],"beneficial":[13,50],"protein":[14,127,155],"variants.":[15,51,79],"However,":[16],"since":[17],"even":[18,123,135,144],"most":[20],"massive":[21],"library":[22,46,83,120,146,167],"contains":[23],"only":[24,133],"a":[25,33,45,55],"miniscule":[26],"fraction":[27],"possible":[30],"variants":[31],"target":[34],"protein,":[35],"it":[36],"is":[37],"advantageous":[38],"to":[39,43,136,152,179],"use":[40],"computational":[41],"methods":[42],"design":[44,121,147],"for":[47,65],"enrichment":[48],"in":[49,129,166],"Here":[52],"we":[53],"develop":[54],"general-purpose":[56],"method,":[57],"OCoM-SOCoM,":[58],"that":[59,171],"designs":[60,84],"large":[61],"simultaneously":[64],"both":[66],"sequence":[68],"properties":[69,74],"(OCoM)":[70],"structural":[73],"(SOCoM)":[75],"their":[77],"constituent":[78],"Our":[80],"algorithm":[81],"optimizes":[82],"along":[85],"continuum":[87],"optimal":[89],"trade-offs":[90],"(the":[91],"Pareto":[92],"frontier)":[93],"between":[94],"library-based":[95],"scores":[96],"efficiently":[97],"assessing":[98],"expected":[99],"structure-based":[100],"energy":[101],"(via":[102,110],"Cluster":[103],"Expansion":[104],"analysis)":[105],"vs.":[106],"sequence-based":[107],"evolutionary":[108],"acceptability":[109],"statistical":[111],"analysis":[112],"homologs).":[114],"Significantly,":[115],"while":[116,182],"combinatorics":[118],"are":[122],"worse":[124],"than":[125],"individual":[126],"design,":[128],"practice":[130],"OCoM-SOCoM":[131,172],"requires":[132],"hours":[134],"optimize":[137],"109-member":[138],"(for":[140],"30":[141],"sites)":[142],"within":[143],"larger":[145],"spaces.":[148],"Case":[149],"study":[150],"applications":[151],"green":[153],"fluorescent":[154],"\u03b2-lactamase":[157],"provide":[158],"insights":[159],"into":[160],"how":[161],"sequence-structure":[162],"relationships":[163],"drive":[164],"differences":[165],"composition,":[168],"demonstrate":[170],"incorporate":[174],"mutations":[175],"previously":[176],"experimentally":[177],"found":[178],"be":[180],"valuable":[181],"also":[183],"providing":[184],"novel":[185],"diverse":[187],"mutational":[188],"combinations.":[189]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2016-12-08T00:00:00"}
