{"id":"https://openalex.org/W3191502010","doi":"https://doi.org/10.1107/s2059798321005891","title":"CCD 2 : design constructs for protein expression, the easy way","display_name":"CCD 2 : design constructs for protein expression, the easy way","publication_year":2021,"publication_date":"2021-07-29","ids":{"openalex":"https://openalex.org/W3191502010","doi":"https://doi.org/10.1107/s2059798321005891","mag":"3191502010","pmid":"https://pubmed.ncbi.nlm.nih.gov/34342272"},"language":"en","primary_location":{"id":"doi:10.1107/s2059798321005891","doi":"https://doi.org/10.1107/s2059798321005891","is_oa":true,"landing_page_url":"https://doi.org/10.1107/s2059798321005891","pdf_url":"https://journals.iucr.org/d/issues/2021/08/00/qg5001/qg5001.pdf","source":{"id":"https://openalex.org/S4393918103","display_name":"Acta Crystallographica Section D Structural Biology","issn_l":"2059-7983","issn":["2059-7983"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-b","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-1"],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Acta Crystallographica Section D Structural Biology","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://journals.iucr.org/d/issues/2021/08/00/qg5001/qg5001.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5067517104","display_name":"A.G. Murachelli","orcid":"https://orcid.org/0000-0003-2968-8972","observed_orcids":["https://orcid.org/0000-0003-2968-8972"]},"institutions":[{"id":"https://openalex.org/I2898336195","display_name":"The Netherlands Cancer Institute","ror":"https://ror.org/03xqtf034","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I2898336195"]},{"id":"https://openalex.org/I4210111138","display_name":"Oncode Institute","ror":"https://ror.org/01n92vv28","country_code":"NL","type":"education","lineage":["https://openalex.org/I4210111138"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Andrea Giovanni Murachelli","raw_affiliation_strings":["Oncode Institute and Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands"],"raw_orcid":"https://orcid.org/0000-0003-2968-8972","affiliations":[{"raw_affiliation_string":"Oncode Institute and Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I2898336195","https://openalex.org/I4210111138"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055572039","display_name":"George Damaskos","orcid":"https://orcid.org/0000-0003-0047-5674","observed_orcids":["https://orcid.org/0000-0003-0047-5674"]},"institutions":[{"id":"https://openalex.org/I2898336195","display_name":"The Netherlands Cancer Institute","ror":"https://ror.org/03xqtf034","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I2898336195"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"George Damaskos","raw_affiliation_strings":["Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands"],"raw_orcid":"https://orcid.org/0000-0003-0047-5674","affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I2898336195"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5014431830","display_name":"Anastassis Perrakis A","orcid":"https://orcid.org/0000-0002-1151-6227","observed_orcids":["https://orcid.org/0000-0002-1151-6227"]},"institutions":[{"id":"https://openalex.org/I2898336195","display_name":"The Netherlands Cancer Institute","ror":"https://ror.org/03xqtf034","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I2898336195"]},{"id":"https://openalex.org/I4210111138","display_name":"Oncode Institute","ror":"https://ror.org/01n92vv28","country_code":"NL","type":"education","lineage":["https://openalex.org/I4210111138"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Anastassis Perrakis","raw_affiliation_strings":["Oncode Institute and Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands"],"raw_orcid":"https://orcid.org/0000-0002-1151-6227","affiliations":[{"raw_affiliation_string":"Oncode Institute and Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I2898336195","https://openalex.org/I4210111138"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3850,"currency":"USD","value_usd":3850},"apc_paid":{"value":3850,"currency":"USD","value_usd":3850},"fwci":0.2173,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.37746131,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":96},"biblio":{"volume":"77","issue":"8","first_page":"992","last_page":"1000"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.8403000235557556,"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"}},"topics":[{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.8403000235557556,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.1559000015258789,"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/T11124","display_name":"Protein purification and stability","score":0.0007999999797903001,"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/protein-truncation","display_name":"protein truncation","score":0.859000027179718},{"id":"https://openalex.org/keywords/recombinant-protein-expression","display_name":"recombinant protein expression","score":0.7459999918937683},{"id":"https://openalex.org/keywords/primer-design","display_name":"primer design","score":0.6880000233650208},{"id":"https://openalex.org/keywords/sequence-conservation","display_name":"sequence conservation","score":0.7329999804496765},{"id":"https://openalex.org/keywords/protein-secondary-structure-prediction","display_name":"secondary structure prediction","score":0.9390000104904175},{"id":"https://openalex.org/keywords/protein-domains","display_name":"protein domains","score":0.7139999866485596},{"id":"https://openalex.org/keywords/intrinsically-disordered-regions","display_name":"intrinsically disordered regions","score":0.9390000104904175},{"id":"https://openalex.org/keywords/post-translational-modification","display_name":"post-translational modification","score":0.9940000176429749},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.8399999737739563},{"id":"https://openalex.org/keywords/structural-biology","display_name":"structural biology","score":0.6930000185966492}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6320005059242249},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.5755476951599121},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.572096049785614},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.5599537491798401},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5264402627944946},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.5075632333755493},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.48623552918434143},{"id":"https://openalex.org/C40767141","wikidata":"https://www.wikidata.org/wiki/Q285697","display_name":"Recombinant DNA","level":3,"score":0.44589802622795105},{"id":"https://openalex.org/C106195933","wikidata":"https://www.wikidata.org/wiki/Q7847935","display_name":"Truncation (statistics)","level":2,"score":0.4284914433956146},{"id":"https://openalex.org/C6856738","wikidata":"https://www.wikidata.org/wiki/Q331672","display_name":"Protein expression","level":3,"score":0.4156857430934906},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3530706763267517},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.34797602891921997},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.253901869058609},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.23181083798408508},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.22764253616333008},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.1588442325592041},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.15781709551811218},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1471771001815796},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.14472275972366333},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1425325572490692},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.13045474886894226},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1107/s2059798321005891","doi":"https://doi.org/10.1107/s2059798321005891","is_oa":true,"landing_page_url":"https://doi.org/10.1107/s2059798321005891","pdf_url":"https://journals.iucr.org/d/issues/2021/08/00/qg5001/qg5001.pdf","source":{"id":"https://openalex.org/S4393918103","display_name":"Acta Crystallographica Section D Structural Biology","issn_l":"2059-7983","issn":["2059-7983"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-b","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-1"],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Acta Crystallographica Section D Structural Biology","raw_type":"journal-article"},{"id":"pmid:34342272","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34342272","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,"listed_in":[],"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":"Acta crystallographica. Section D, Structural biology","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8329859","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8329859","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Acta Crystallogr D Struct Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1107/s2059798321005891","doi":"https://doi.org/10.1107/s2059798321005891","is_oa":true,"landing_page_url":"https://doi.org/10.1107/s2059798321005891","pdf_url":"https://journals.iucr.org/d/issues/2021/08/00/qg5001/qg5001.pdf","source":{"id":"https://openalex.org/S4393918103","display_name":"Acta Crystallographica Section D Structural Biology","issn_l":"2059-7983","issn":["2059-7983"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-b","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-1"],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Acta Crystallographica Section D Structural Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"sustainable_development_goals_aurora":[{"score":0.5099999904632568,"id":"https://metadata.un.org/sdg/15","display_name":"Life on land"}],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3191502010.pdf","grobid_xml":"https://content.openalex.org/works/W3191502010.grobid-xml"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W1974719543","https://openalex.org/W1990300808","https://openalex.org/W1995808589","https://openalex.org/W2003847336","https://openalex.org/W2014776147","https://openalex.org/W2024645073","https://openalex.org/W2025391446","https://openalex.org/W2055043387","https://openalex.org/W2055193239","https://openalex.org/W2075651068","https://openalex.org/W2081856012","https://openalex.org/W2094476648","https://openalex.org/W2121058712","https://openalex.org/W2132926880","https://openalex.org/W2133142974","https://openalex.org/W2137015675","https://openalex.org/W2142678478","https://openalex.org/W2150271494","https://openalex.org/W2161199282","https://openalex.org/W2294054088","https://openalex.org/W2898402099","https://openalex.org/W2994150660","https://openalex.org/W3093868212","https://openalex.org/W3116711270","https://openalex.org/W3136918052","https://openalex.org/W4244736178"],"related_works":["https://openalex.org/W2366107444","https://openalex.org/W2274607931","https://openalex.org/W4388145910","https://openalex.org/W1976205134","https://openalex.org/W2381570729","https://openalex.org/W4248336175","https://openalex.org/W3009369890","https://openalex.org/W2897634435","https://openalex.org/W4388280821","https://openalex.org/W2385316441"],"abstract_inverted_index":{"Studying":[0],"the":[1,9,44,75,87,95,113,116],"function":[2],"or":[3],"structure":[4,57],"of":[5,11,112,115,129,156],"proteins":[6],"usually":[7],"requires":[8],"generation":[10],"many":[12],"protein-truncation":[13],"constructs":[14,91],"for":[15,89,98,125,145,153,161],"recombinant":[16,150],"expression,":[17],"which":[18],"is":[19,27],"a":[20,28,109,142],"tedious":[21],"and":[22,34,60,65,92,158],"error-prone":[23],"job.":[24],"CCD":[25,38,79,106,130],"2":[26,39,80,107,131],"software":[29],"tool":[30,144],"designed":[31],"to":[32,47,84],"facilitate":[33],"automate":[35],"this":[36],"task.":[37],"helps":[40],"scientists":[41],"by":[42,101,135],"aggregating":[43],"information":[45,52,66],"necessary":[46,97],"design":[48],"protein-expression":[49],"constructs.":[50],"This":[51],"includes":[53],"sequence":[54],"conservation,":[55],"secondary":[56],"prediction,":[58],"domain(s)":[59],"disorder":[61],"detection,":[62],"post-translational":[63],"modifications":[64],"on":[67],"similar":[68],"(domain)":[69],"structures":[70],"that":[71,138,147],"are":[72,132],"available":[73],"in":[74,149,159],"Protein":[76],"Data":[77],"Bank.":[78],"then":[81],"allows":[82],"users":[83],"easily":[85],"choose":[86],"boundaries":[88],"protein":[90,151],"automatically":[93],"generates":[94],"primers":[96],"construct":[99],"amplification":[100],"polymerase":[102],"chain":[103],"reaction.":[104],"Finally,":[105],"provides":[108],"quick":[110],"analysis":[111],"properties":[114],"chosen":[117],"constructs,":[118],"together":[119],"with":[120],"their":[121],"DNA":[122],"vector":[123],"maps":[124],"bookkeeping.":[126],"The":[127],"features":[128],"discussed":[133],"step":[134],"step,":[136],"showing":[137],"it":[139],"can":[140],"be":[141],"useful":[143],"laboratories":[146],"engage":[148],"production":[152],"any":[154],"type":[155],"experiment,":[157],"particular":[160],"structural":[162],"biology":[163],"studies.":[164]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1}],"updated_date":"2026-10-14T16:39:01.820549","created_date":"2021-08-16T00:00:00"}
