{"id":"https://openalex.org/W2113668329","doi":"https://doi.org/10.1186/1758-2946-2-s1-o4","title":"Representation and searching of biomolecules","display_name":"Representation and searching of biomolecules","publication_year":2010,"publication_date":"2010-05-01","ids":{"openalex":"https://openalex.org/W2113668329","doi":"https://doi.org/10.1186/1758-2946-2-s1-o4","mag":"2113668329"},"language":"en","primary_location":{"id":"doi:10.1186/1758-2946-2-s1-o4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-2-s1-o4","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-2-S1-O4","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-2-S1-O4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5111904911","display_name":"Joeseph L Durant","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Joeseph L Durant","raw_affiliation_strings":["Symyx Technologies, 2440 Camino Ramon, San Ramon, California, USA","Symyx Technologies, San Ramon, USA"],"affiliations":[{"raw_affiliation_string":"Symyx Technologies, 2440 Camino Ramon, San Ramon, California, USA","institution_ids":[]},{"raw_affiliation_string":"Symyx Technologies, San Ramon, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110209912","display_name":"WL Chen","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"WL Chen","raw_affiliation_strings":["Symyx Technologies, 2440 Camino Ramon, San Ramon, California, USA","Symyx Technologies, San Ramon, USA"],"affiliations":[{"raw_affiliation_string":"Symyx Technologies, 2440 Camino Ramon, San Ramon, California, USA","institution_ids":[]},{"raw_affiliation_string":"Symyx Technologies, San Ramon, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110209913","display_name":"B. Christie","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"BD Christie","raw_affiliation_strings":["Symyx Technologies, 2440 Camino Ramon, San Ramon, California, USA","Symyx Technologies, San Ramon, USA"],"affiliations":[{"raw_affiliation_string":"Symyx Technologies, 2440 Camino Ramon, San Ramon, California, USA","institution_ids":[]},{"raw_affiliation_string":"Symyx Technologies, San Ramon, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053774383","display_name":"DL Grier","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"DL Grier","raw_affiliation_strings":["Symyx Technologies, 2440 Camino Ramon, San Ramon, California, USA","Symyx Technologies, San Ramon, USA"],"affiliations":[{"raw_affiliation_string":"Symyx Technologies, 2440 Camino Ramon, San Ramon, California, USA","institution_ids":[]},{"raw_affiliation_string":"Symyx Technologies, San Ramon, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018930951","display_name":"BA Leland","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"BA Leland","raw_affiliation_strings":["Symyx Technologies, 2440 Camino Ramon, San Ramon, California, USA","Symyx Technologies, San Ramon, USA"],"affiliations":[{"raw_affiliation_string":"Symyx Technologies, 2440 Camino Ramon, San Ramon, California, USA","institution_ids":[]},{"raw_affiliation_string":"Symyx Technologies, San Ramon, USA","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5014091376","display_name":"JG Nourse","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"JG Nourse","raw_affiliation_strings":["Symyx Technologies, 2440 Camino Ramon, San Ramon, California, USA","Symyx Technologies, San Ramon, USA"],"affiliations":[{"raw_affiliation_string":"Symyx Technologies, 2440 Camino Ramon, San Ramon, California, USA","institution_ids":[]},{"raw_affiliation_string":"Symyx Technologies, San Ramon, USA","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5111904911"],"corresponding_institution_ids":[],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":0.0,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.13505814,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"2","issue":"S1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10908","display_name":"Analytical Chemistry and Chromatography","score":0.9979000091552734,"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"}},"topics":[{"id":"https://openalex.org/T10908","display_name":"Analytical Chemistry and Chromatography","score":0.9979000091552734,"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"}},{"id":"https://openalex.org/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9944000244140625,"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/T11407","display_name":"Innovative Microfluidic and Catalytic Techniques Innovation","score":0.9761999845504761,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/biomolecule","display_name":"Biomolecule","score":0.853224515914917},{"id":"https://openalex.org/keywords/template","display_name":"Template","score":0.7899219989776611},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6520012617111206},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.6102940440177917},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5295881628990173},{"id":"https://openalex.org/keywords/tree-traversal","display_name":"Tree traversal","score":0.5005502700805664},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.40014833211898804},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3846238851547241},{"id":"https://openalex.org/keywords/nanotechnology","display_name":"Nanotechnology","score":0.28858715295791626},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.26226261258125305},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.14525428414344788},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.09593445062637329}],"concepts":[{"id":"https://openalex.org/C49853544","wikidata":"https://www.wikidata.org/wiki/Q206229","display_name":"Biomolecule","level":2,"score":0.853224515914917},{"id":"https://openalex.org/C82714645","wikidata":"https://www.wikidata.org/wiki/Q438331","display_name":"Template","level":2,"score":0.7899219989776611},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6520012617111206},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.6102940440177917},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5295881628990173},{"id":"https://openalex.org/C140745168","wikidata":"https://www.wikidata.org/wiki/Q1210082","display_name":"Tree traversal","level":2,"score":0.5005502700805664},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.40014833211898804},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3846238851547241},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.28858715295791626},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.26226261258125305},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.14525428414344788},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.09593445062637329},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/1758-2946-2-s1-o4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-2-s1-o4","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-2-S1-O4","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:a0f96615f1994bc3a59ebd550581798b","is_oa":true,"landing_page_url":"https://doaj.org/article/a0f96615f1994bc3a59ebd550581798b","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 2, Iss Suppl 1, p O4 (2010)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2867135","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2867135","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Cheminform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1758-2946-2-s1-o4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-2-s1-o4","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-2-S1-O4","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2113668329.pdf","grobid_xml":"https://content.openalex.org/works/W2113668329.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2136735429","https://openalex.org/W170547082","https://openalex.org/W2587876411","https://openalex.org/W2358332176","https://openalex.org/W4229950834","https://openalex.org/W4301044568","https://openalex.org/W2128075414","https://openalex.org/W1587123803","https://openalex.org/W2571039174","https://openalex.org/W2952867832"],"abstract_inverted_index":{"Biomolecules":[0],"present":[1,239],"challenges":[2],"to":[3,14,53,89,151,204,236],"chemical":[4,26],"information":[5],"systems":[6],"designed":[7],"for":[8,58,62,72,85,139,162],"small":[9],"molecules.":[10],"Their":[11],"sizes,":[12],"up":[13,36],"tens":[15],"of":[16,18,28,37,40,44,83,95,106,128,143,160,196,210,216,227,233,247],"thousands":[17],"atoms,":[19],"overwhelm":[20],"representation/storage/searching":[21],"solutions":[22],"built":[23],"on":[24],"explicit":[25,91,96,112,131,145,149],"representation":[27,57,71],"the":[29,63,79,102,107,137,141,187],"structures.":[30],"But":[31],"biomolecules":[32,59],"are":[33,98,114,134,184],"largely":[34],"made":[35],"many":[38],"repeats":[39],"a":[41,47,55,68,167,190,213,228],"limited":[42,126],"number":[43,127],"building-block":[45],"molecules,":[46],"fact":[48],"which":[49,86],"has":[50],"been":[51],"used":[52],"provide":[54],"compressed":[56],"using":[60,148],"templates":[61,200],"building":[64],"blocks.\r\n\r\nWe":[65],"have":[66,220],"adopted":[67],"modified":[69,81,153],"template-based":[70],"biomolecules.":[73],"Our":[74],"primary":[75],"interest":[76],"is":[77],"in":[78,101,136],"chemically":[80],"portions":[82,105],"biomolecules,":[84],"we":[87,155],"choose":[88],"use":[90,195],"chemistry.":[92],"These":[93],"areas":[94],"chemistry":[97,113,132,150],"then":[99],"embedded":[100],"template-compressed,":[103],"unmodified":[104],"full":[108],"biomolecule.\r\n\r\nThe":[109],"regions":[110,133,154],"containing":[111,212],"indexed,":[115],"and":[116,177,181,207,242],"thus":[117],"can":[118,156],"be":[119,205],"structure":[120,188],"searched":[121],"with":[122,186],"good":[123],"performance.":[124],"A":[125],"residues":[129,219],"surrounding":[130],"included":[135],"index":[138],"searching":[140],"context":[142],"these":[144],"regions.":[146],"By":[147],"represent":[152],"search":[157,170],"across":[158],"classes":[159],"modifications":[161],"common":[163],"features.":[164],"For":[165],"example":[166,240],"single":[168],"substructure":[169],"query":[171],"will":[172,238],"find":[173],"green":[174],"fluorescent":[175],"protein,":[176],"its":[178],"histidine,":[179],"phenylalanine":[180],"tryptophan":[182],"analogs.\r\n\r\nTemplates":[183],"stored":[185],"providing":[189],"self-contained":[191],"file":[192],"format.":[193],"The":[194,218],"NEMA":[197],"keys":[198],"allows":[199,208],"from":[201],"different":[202],"structures":[203,211,241],"compared,":[206],"storage":[209],"canonical":[214],"list":[215],"templates.":[217],"defined":[221],"attachment":[222],"points,":[223],"allowing":[224],"automated":[225],"traversal":[226],"protein":[229],"backbone,":[230],"or":[231],"location":[232],"non-backbone":[234],"bonds":[235],"residues.\r\n\r\nWe":[237],"structural":[243],"queries":[244],"highlighting":[245],"capabilities":[246],"our":[248],"representation.":[249]},"counts_by_year":[{"year":2020,"cited_by_count":1}],"updated_date":"2026-03-17T17:19:04.345684","created_date":"2025-10-10T00:00:00"}
