{"id":"https://openalex.org/W4366991602","doi":"https://doi.org/10.1186/s12859-023-05296-y","title":"CRISPR-Cas-Docker: web-based in silico docking and machine learning-based classification of crRNAs with Cas proteins","display_name":"CRISPR-Cas-Docker: web-based in silico docking and machine learning-based classification of crRNAs with Cas proteins","publication_year":2023,"publication_date":"2023-04-25","ids":{"openalex":"https://openalex.org/W4366991602","doi":"https://doi.org/10.1186/s12859-023-05296-y","pmid":"https://pubmed.ncbi.nlm.nih.gov/37098485"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-023-05296-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05296-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05296-y","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05296-y","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5081670766","display_name":"Ho-min Park","orcid":"https://orcid.org/0000-0001-9937-8617"},"institutions":[{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]},{"id":"https://openalex.org/I4210132857","display_name":"Ghent University Global Campus","ror":"https://ror.org/041bygf77","country_code":"KR","type":"education","lineage":["https://openalex.org/I32597200","https://openalex.org/I4210132857"]}],"countries":["BE","KR"],"is_corresponding":false,"raw_author_name":"Ho-min Park","raw_affiliation_strings":["Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon, 21985, South Korea","Department of Electronics and Information Systems, Ghent University, 9000, Ghent, Belgium","Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon, South Korea","Department of Electronics and Information Systems, Ghent University, Ghent, Belgium"],"raw_orcid":"https://orcid.org/0000-0001-9937-8617","affiliations":[{"raw_affiliation_string":"Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon, 21985, South Korea","institution_ids":["https://openalex.org/I4210132857"]},{"raw_affiliation_string":"Department of Electronics and Information Systems, Ghent University, 9000, Ghent, Belgium","institution_ids":["https://openalex.org/I32597200"]},{"raw_affiliation_string":"Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon, South Korea","institution_ids":["https://openalex.org/I4210132857"]},{"raw_affiliation_string":"Department of Electronics and Information Systems, Ghent University, Ghent, Belgium","institution_ids":["https://openalex.org/I32597200"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035742249","display_name":"Jongbum Won","orcid":"https://orcid.org/0009-0001-5650-3315"},"institutions":[{"id":"https://openalex.org/I4210132857","display_name":"Ghent University Global Campus","ror":"https://ror.org/041bygf77","country_code":"KR","type":"education","lineage":["https://openalex.org/I32597200","https://openalex.org/I4210132857"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Jongbum Won","raw_affiliation_strings":["Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon, 21985, South Korea","Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon, South Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon, 21985, South Korea","institution_ids":["https://openalex.org/I4210132857"]},{"raw_affiliation_string":"Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon, South Korea","institution_ids":["https://openalex.org/I4210132857"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090864953","display_name":"Yunseol Park","orcid":"https://orcid.org/0000-0002-2005-1847"},"institutions":[{"id":"https://openalex.org/I4210132857","display_name":"Ghent University Global Campus","ror":"https://ror.org/041bygf77","country_code":"KR","type":"education","lineage":["https://openalex.org/I32597200","https://openalex.org/I4210132857"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Yunseol Park","raw_affiliation_strings":["Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon, 21985, South Korea","Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon, South Korea"],"raw_orcid":"https://orcid.org/0000-0002-2005-1847","affiliations":[{"raw_affiliation_string":"Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon, 21985, South Korea","institution_ids":["https://openalex.org/I4210132857"]},{"raw_affiliation_string":"Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon, South Korea","institution_ids":["https://openalex.org/I4210132857"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068577161","display_name":"Esla Timothy Anzaku","orcid":"https://orcid.org/0009-0005-7723-159X"},"institutions":[{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]},{"id":"https://openalex.org/I4210132857","display_name":"Ghent University Global Campus","ror":"https://ror.org/041bygf77","country_code":"KR","type":"education","lineage":["https://openalex.org/I32597200","https://openalex.org/I4210132857"]}],"countries":["BE","KR"],"is_corresponding":false,"raw_author_name":"Esla Timothy Anzaku","raw_affiliation_strings":["Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon, 21985, South Korea","Department of Electronics and Information Systems, Ghent University, 9000, Ghent, Belgium","Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon, South Korea","Department of Electronics and Information Systems, Ghent University, Ghent, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon, 21985, South Korea","institution_ids":["https://openalex.org/I4210132857"]},{"raw_affiliation_string":"Department of Electronics and Information Systems, Ghent University, 9000, Ghent, Belgium","institution_ids":["https://openalex.org/I32597200"]},{"raw_affiliation_string":"Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon, South Korea","institution_ids":["https://openalex.org/I4210132857"]},{"raw_affiliation_string":"Department of Electronics and Information Systems, Ghent University, Ghent, Belgium","institution_ids":["https://openalex.org/I32597200"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012688473","display_name":"Joris Vankerschaver","orcid":"https://orcid.org/0000-0002-5813-5659"},"institutions":[{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]},{"id":"https://openalex.org/I4210132857","display_name":"Ghent University Global Campus","ror":"https://ror.org/041bygf77","country_code":"KR","type":"education","lineage":["https://openalex.org/I32597200","https://openalex.org/I4210132857"]}],"countries":["BE","KR"],"is_corresponding":false,"raw_author_name":"Joris Vankerschaver","raw_affiliation_strings":["Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon, 21985, South Korea","Department of Applied Mathematics, Computer Science and Statistics, Ghent University, 9000, Ghent, Belgium","Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon, South Korea","Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium"],"raw_orcid":"https://orcid.org/0000-0002-5813-5659","affiliations":[{"raw_affiliation_string":"Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon, 21985, South Korea","institution_ids":["https://openalex.org/I4210132857"]},{"raw_affiliation_string":"Department of Applied Mathematics, Computer Science and Statistics, Ghent University, 9000, Ghent, Belgium","institution_ids":["https://openalex.org/I32597200"]},{"raw_affiliation_string":"Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon, South Korea","institution_ids":["https://openalex.org/I4210132857"]},{"raw_affiliation_string":"Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium","institution_ids":["https://openalex.org/I32597200"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077912411","display_name":"Arnout Van Messem","orcid":"https://orcid.org/0000-0001-8545-7437"},"institutions":[{"id":"https://openalex.org/I157674565","display_name":"University of Li\u00e8ge","ror":"https://ror.org/00afp2z80","country_code":"BE","type":"education","lineage":["https://openalex.org/I157674565"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Arnout Van Messem","raw_affiliation_strings":["Department of Mathematics, University of Li\u00e8ge, 4000, Li\u00e8ge, Belgium","Department of Mathematics, University of Li\u00e8ge, Li\u00e8ge, Belgium"],"raw_orcid":"https://orcid.org/0000-0001-8545-7437","affiliations":[{"raw_affiliation_string":"Department of Mathematics, University of Li\u00e8ge, 4000, Li\u00e8ge, Belgium","institution_ids":["https://openalex.org/I157674565"]},{"raw_affiliation_string":"Department of Mathematics, University of Li\u00e8ge, Li\u00e8ge, Belgium","institution_ids":["https://openalex.org/I157674565"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029555436","display_name":"Wesley De Neve","orcid":"https://orcid.org/0000-0002-8190-3839"},"institutions":[{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]},{"id":"https://openalex.org/I4210132857","display_name":"Ghent University Global Campus","ror":"https://ror.org/041bygf77","country_code":"KR","type":"education","lineage":["https://openalex.org/I32597200","https://openalex.org/I4210132857"]}],"countries":["BE","KR"],"is_corresponding":false,"raw_author_name":"Wesley De Neve","raw_affiliation_strings":["Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon, 21985, South Korea","Department of Electronics and Information Systems, Ghent University, 9000, Ghent, Belgium","Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon, South Korea","Department of Electronics and Information Systems, Ghent University, Ghent, Belgium"],"raw_orcid":"https://orcid.org/0000-0002-8190-3839","affiliations":[{"raw_affiliation_string":"Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon, 21985, South Korea","institution_ids":["https://openalex.org/I4210132857"]},{"raw_affiliation_string":"Department of Electronics and Information Systems, Ghent University, 9000, Ghent, Belgium","institution_ids":["https://openalex.org/I32597200"]},{"raw_affiliation_string":"Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon, South Korea","institution_ids":["https://openalex.org/I4210132857"]},{"raw_affiliation_string":"Department of Electronics and Information Systems, Ghent University, Ghent, Belgium","institution_ids":["https://openalex.org/I32597200"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5084547030","display_name":"Hyunjin Shim","orcid":"https://orcid.org/0000-0002-7052-0971"},"institutions":[{"id":"https://openalex.org/I4210132857","display_name":"Ghent University Global Campus","ror":"https://ror.org/041bygf77","country_code":"KR","type":"education","lineage":["https://openalex.org/I32597200","https://openalex.org/I4210132857"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"Hyunjin Shim","raw_affiliation_strings":["Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon, 21985, South Korea. hyunjin.shim@ghent.ac.kr","Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon, South Korea"],"raw_orcid":"https://orcid.org/0000-0002-7052-0971","affiliations":[{"raw_affiliation_string":"Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon, 21985, South Korea. hyunjin.shim@ghent.ac.kr","institution_ids":["https://openalex.org/I4210132857"]},{"raw_affiliation_string":"Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon, South Korea","institution_ids":["https://openalex.org/I4210132857"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5084547030"],"corresponding_institution_ids":["https://openalex.org/I4210132857"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.371,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.5342252,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"24","issue":"1","first_page":"167","last_page":"167"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9688000082969666,"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":0.9688000082969666,"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/T10604","display_name":"RNA Research and Splicing","score":0.003599999938160181,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.0024999999441206455,"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/crispr","display_name":"CRISPR","score":0.9074544906616211},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.8589433431625366},{"id":"https://openalex.org/keywords/trans-activating-crrna","display_name":"Trans-activating crRNA","score":0.7099418044090271},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6663477420806885},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.642184853553772},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.5656242370605469},{"id":"https://openalex.org/keywords/cas9","display_name":"Cas9","score":0.3626563549041748},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3219594657421112},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.18933424353599548},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.14056232571601868},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1363849937915802},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13021722435951233}],"concepts":[{"id":"https://openalex.org/C98108389","wikidata":"https://www.wikidata.org/wiki/Q412563","display_name":"CRISPR","level":3,"score":0.9074544906616211},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.8589433431625366},{"id":"https://openalex.org/C84356384","wikidata":"https://www.wikidata.org/wiki/Q7833575","display_name":"Trans-activating crRNA","level":5,"score":0.7099418044090271},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6663477420806885},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.642184853553772},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.5656242370605469},{"id":"https://openalex.org/C132455925","wikidata":"https://www.wikidata.org/wiki/Q16965677","display_name":"Cas9","level":4,"score":0.3626563549041748},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3219594657421112},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.18933424353599548},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.14056232571601868},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1363849937915802},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13021722435951233}],"mesh":[{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064113","descriptor_name":"CRISPR-Cas Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064113","descriptor_name":"CRISPR-Cas Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064113","descriptor_name":"CRISPR-Cas Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1186/s12859-023-05296-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05296-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05296-y","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37098485","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37098485","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,"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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:archive.ugent.be:01H1XVGFRGDDDNNRJW1QRNFN4G","is_oa":true,"landing_page_url":"https://biblio.ugent.be/publication/01H1XVGFRGDDDNNRJW1QRNFN4G","pdf_url":"https://biblio.ugent.be/publication/01H1XVGFRGDDDNNRJW1QRNFN4G/file/01H1XVH90DV87776TKJXNNZY0J.pdf","source":{"id":"https://openalex.org/S4306400478","display_name":"Ghent University Academic Bibliography (Ghent University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I32597200","host_organization_name":"Ghent University","host_organization_lineage":["https://openalex.org/I32597200"],"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":"ISSN: 1471-2105","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:orbi.ulg.ac.be:2268/302125","is_oa":true,"landing_page_url":"https://orbi.uliege.be/handle/2268/302125","pdf_url":"https://orbi.uliege.be/bitstream/2268/302125/1/s12859-023-05296-y.pdf","source":{"id":"https://openalex.org/S4306400651","display_name":"Open Repository and Bibliography (University of Li\u00e8ge)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I157674565","host_organization_name":"University of Li\u00e8ge","host_organization_lineage":["https://openalex.org/I157674565"],"host_organization_lineage_names":[],"type":"repository"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, 24 (1), 167 (2023-04-25)","raw_type":"http://purl.org/coar/resource_type/c_6501"},{"id":"pmh:oai:pubmedcentral.nih.gov:10127312","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10127312","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10127312/pdf/12859_2023_Article_5296.pdf","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,"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":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:722e0901285745c1a1937105abefba2a","is_oa":true,"landing_page_url":"https://doaj.org/article/722e0901285745c1a1937105abefba2a","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 24, Iss 1, Pp 1-6 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-023-05296-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05296-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05296-y","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320322603","display_name":"Universiteit Gent","ror":"https://ror.org/00cv9y106"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4366991602.pdf"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W14498347","https://openalex.org/W1981185465","https://openalex.org/W1990487336","https://openalex.org/W2045435533","https://openalex.org/W2064815984","https://openalex.org/W2090211843","https://openalex.org/W2123965484","https://openalex.org/W2130479394","https://openalex.org/W2164059036","https://openalex.org/W2199695484","https://openalex.org/W2530493445","https://openalex.org/W2602907179","https://openalex.org/W2803245377","https://openalex.org/W2907803369","https://openalex.org/W2921079059","https://openalex.org/W2995081665","https://openalex.org/W3015438624","https://openalex.org/W3019944201","https://openalex.org/W3177828909","https://openalex.org/W3194531251","https://openalex.org/W3199041041","https://openalex.org/W4220803716","https://openalex.org/W4285744239","https://openalex.org/W4303427239"],"related_works":["https://openalex.org/W930226034","https://openalex.org/W4285586845","https://openalex.org/W2473112503","https://openalex.org/W2463802462","https://openalex.org/W2936470333","https://openalex.org/W4292092820","https://openalex.org/W3003269839","https://openalex.org/W3136862730","https://openalex.org/W2974814723","https://openalex.org/W4366991602"],"abstract_inverted_index":{"BACKGROUND:":[0],"CRISPR-Cas-Docker":[1,49,107,133],"is":[2,134],"a":[3,60,64,71,139],"web":[4,19,140],"server":[5,20],"for":[6,101,130],"in":[7,45,102,119],"silico":[8,68,103,120],"docking":[9,104],"experiments":[10],"with":[11,25],"CRISPR":[12,37],"RNAs":[13],"(crRNAs)":[14],"and":[15,39,70,127,142],"Cas":[16,40,57],"proteins.":[17],"This":[18],"aims":[21],"at":[22,136,143],"providing":[23],"experimentalists":[24],"the":[26,55,78,109,112],"optimal":[27,56],"crRNA-Cas":[28],"pair":[29],"predicted":[30],"computationally":[31],"when":[32],"prokaryotic":[33],"genomes":[34],"have":[35],"multiple":[36,123],"arrays":[38],"systems,":[41],"as":[42,138,145],"frequently":[43],"observed":[44],"metagenomic":[46],"data.":[47],"RESULTS:":[48],"provides":[50],"two":[51],"methods":[52],"to":[53,97,115],"predict":[54,116],"protein":[58],"given":[59],"particular":[61],"crRNA":[62],"sequence:":[63],"structure-based":[65,79],"method":[66,73],"(in":[67],"docking)":[69],"sequence-based":[72],"(machine":[74],"learning":[75],"classification).":[76],"For":[77],"method,":[80],"users":[81],"can":[82],"either":[83],"provide":[84],"experimentally":[85],"determined":[86],"3D":[87],"structures":[88,100],"of":[89,111,125],"these":[90],"macromolecules":[91],"or":[92],"use":[93],"an":[94,146],"integrated":[95],"pipeline":[96],"generate":[98],"3D-predicted":[99],"experiments.":[105],"CONCLUSION:":[106],"addresses":[108],"need":[110],"CRISPR-Cas":[113,131],"community":[114],"RNA-protein":[117],"interactions":[118],"by":[121],"optimizing":[122],"stages":[124],"computation":[126],"evaluation,":[128],"specifically":[129],"systems.":[132],"available":[135],"www.crisprcasdocker.org":[137],"server,":[141],"https://github.com/hshimlab/CRISPR-Cas-Docker":[144],"open-source":[147],"tool.":[148]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
