{"id":"https://openalex.org/W4366464000","doi":"https://doi.org/10.1093/bib/bbad133","title":"Decoding CRISPR\u2013Cas PAM recognition with UniDesign","display_name":"Decoding CRISPR\u2013Cas PAM recognition with UniDesign","publication_year":2023,"publication_date":"2023-03-16","ids":{"openalex":"https://openalex.org/W4366464000","doi":"https://doi.org/10.1093/bib/bbad133","pmid":"https://pubmed.ncbi.nlm.nih.gov/37078688"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad133","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbad133","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10199764/pdf/bbad133.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5072178740","display_name":"Xiaoqiang Huang","orcid":"https://orcid.org/0000-0002-1005-848X"},"institutions":[{"id":"https://openalex.org/I4210117557","display_name":"Michigan Center for Translational Pathology","ror":"https://ror.org/027t4kk23","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210114445","https://openalex.org/I4210117557"]},{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Xiaoqiang Huang","raw_affiliation_strings":["Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical School , 2800 Plymouth Road, Ann Arbor, MI 48109 , USA"],"affiliations":[{"raw_affiliation_string":"Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical School , 2800 Plymouth Road, Ann Arbor, MI 48109 , USA","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210117557"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006110795","display_name":"Jun Zhou","orcid":"https://orcid.org/0000-0002-2576-7692"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]},{"id":"https://openalex.org/I4210117557","display_name":"Michigan Center for Translational Pathology","ror":"https://ror.org/027t4kk23","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210114445","https://openalex.org/I4210117557"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jun Zhou","raw_affiliation_strings":["Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical School , 2800 Plymouth Road, Ann Arbor, MI 48109 , USA"],"affiliations":[{"raw_affiliation_string":"Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical School , 2800 Plymouth Road, Ann Arbor, MI 48109 , USA","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210117557"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007667712","display_name":"Dongshan Yang","orcid":"https://orcid.org/0000-0003-2449-8651"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]},{"id":"https://openalex.org/I4210117557","display_name":"Michigan Center for Translational Pathology","ror":"https://ror.org/027t4kk23","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210114445","https://openalex.org/I4210117557"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dongshan Yang","raw_affiliation_strings":["Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical School , 2800 Plymouth Road, Ann Arbor, MI 48109 , USA"],"affiliations":[{"raw_affiliation_string":"Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical School , 2800 Plymouth Road, Ann Arbor, MI 48109 , USA","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210117557"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100784039","display_name":"Jifeng Zhang","orcid":"https://orcid.org/0000-0001-5161-4705"},"institutions":[{"id":"https://openalex.org/I4210117557","display_name":"Michigan Center for Translational Pathology","ror":"https://ror.org/027t4kk23","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210114445","https://openalex.org/I4210117557"]},{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jifeng Zhang","raw_affiliation_strings":["Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical School , 2800 Plymouth Road, Ann Arbor, MI 48109 , USA"],"affiliations":[{"raw_affiliation_string":"Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical School , 2800 Plymouth Road, Ann Arbor, MI 48109 , USA","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210117557"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101862876","display_name":"Xiaofeng Xia","orcid":"https://orcid.org/0000-0001-9522-7459"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Xiaofeng Xia","raw_affiliation_strings":["Research & Development, ATGC Inc. , 100 E Lancaster Avenue, LIMR Building Lab 129, Wynnewood, PA 19096 , USA"],"affiliations":[{"raw_affiliation_string":"Research & Development, ATGC Inc. , 100 E Lancaster Avenue, LIMR Building Lab 129, Wynnewood, PA 19096 , USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007976180","display_name":"Y. Eugene Chen","orcid":"https://orcid.org/0000-0003-2357-7825"},"institutions":[{"id":"https://openalex.org/I4210117557","display_name":"Michigan Center for Translational Pathology","ror":"https://ror.org/027t4kk23","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210114445","https://openalex.org/I4210117557"]},{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yuqing Eugene Chen","raw_affiliation_strings":["Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical School , 2800 Plymouth Road, Ann Arbor, MI 48109 , USA"],"affiliations":[{"raw_affiliation_string":"Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical School , 2800 Plymouth Road, Ann Arbor, MI 48109 , USA","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210117557"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5008649792","display_name":"Jie Xu","orcid":"https://orcid.org/0000-0001-9452-2878"},"institutions":[{"id":"https://openalex.org/I4210117557","display_name":"Michigan Center for Translational Pathology","ror":"https://ror.org/027t4kk23","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210114445","https://openalex.org/I4210117557"]},{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jie Xu","raw_affiliation_strings":["Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical School , 2800 Plymouth Road, Ann Arbor, MI 48109 , USA"],"affiliations":[{"raw_affiliation_string":"Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical School , 2800 Plymouth Road, Ann Arbor, MI 48109 , USA","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210117557"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5007976180","https://openalex.org/A5008649792","https://openalex.org/A5072178740"],"corresponding_institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210117557"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":2.1633,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.87330933,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"24","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10878","display_name":"CRISPR and Genetic Engineering","score":1.0,"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":1.0,"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":0.9289000034332275,"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":0.8077947497367859},{"id":"https://openalex.org/keywords/decoding-methods","display_name":"Decoding methods","score":0.7087536454200745},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5834511518478394},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.37830230593681335},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22253060340881348},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.22248461842536926},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09446266293525696},{"id":"https://openalex.org/keywords/telecommunications","display_name":"Telecommunications","score":0.07384654879570007}],"concepts":[{"id":"https://openalex.org/C98108389","wikidata":"https://www.wikidata.org/wiki/Q412563","display_name":"CRISPR","level":3,"score":0.8077947497367859},{"id":"https://openalex.org/C57273362","wikidata":"https://www.wikidata.org/wiki/Q576722","display_name":"Decoding methods","level":2,"score":0.7087536454200745},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5834511518478394},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.37830230593681335},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22253060340881348},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.22248461842536926},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09446266293525696},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.07384654879570007}],"mesh":[{"descriptor_ui":"D000072669","descriptor_name":"Gene Editing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072669","descriptor_name":"Gene Editing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072669","descriptor_name":"Gene Editing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072669","descriptor_name":"Gene Editing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072669","descriptor_name":"Gene Editing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072669","descriptor_name":"Gene Editing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009696","descriptor_name":"Nucleic Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009696","descriptor_name":"Nucleic Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009696","descriptor_name":"Nucleic Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009696","descriptor_name":"Nucleic Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009696","descriptor_name":"Nucleic Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009696","descriptor_name":"Nucleic Acids","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},{"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},{"descriptor_ui":"D064113","descriptor_name":"CRISPR-Cas Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbad133","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbad133","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37078688","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37078688","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10199764","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10199764","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10199764/pdf/bbad133.pdf","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":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:10199764","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10199764","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10199764/pdf/bbad133.pdf","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":"Brief Bioinform","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1592212554","display_name":null,"funder_award_id":"GM149016","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2547165195","display_name":null,"funder_award_id":"GM122181","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2847489532","display_name":null,"funder_award_id":"HL159871","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3279462294","display_name":null,"funder_award_id":"HL159900","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5338272299","display_name":null,"funder_award_id":"XU19XX0","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5755426514","display_name":null,"funder_award_id":"XU19XX0","funder_id":"https://openalex.org/F4320306168","funder_display_name":"Cystic Fibrosis Foundation"},{"id":"https://openalex.org/G6535812720","display_name":null,"funder_award_id":"HL147527","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306168","display_name":"Cystic Fibrosis Foundation","ror":"https://ror.org/00ax59295"},{"id":"https://openalex.org/F4320309652","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4366464000.pdf","grobid_xml":"https://content.openalex.org/works/W4366464000.grobid-xml"},"referenced_works_count":62,"referenced_works":["https://openalex.org/W1922040927","https://openalex.org/W1970196890","https://openalex.org/W1988101725","https://openalex.org/W2047544230","https://openalex.org/W2059363769","https://openalex.org/W2064815984","https://openalex.org/W2070614858","https://openalex.org/W2089589904","https://openalex.org/W2096261947","https://openalex.org/W2103622571","https://openalex.org/W2107959600","https://openalex.org/W2109154308","https://openalex.org/W2118233996","https://openalex.org/W2149480270","https://openalex.org/W2158266834","https://openalex.org/W2158637234","https://openalex.org/W2162166182","https://openalex.org/W2165869860","https://openalex.org/W2172425918","https://openalex.org/W2201713963","https://openalex.org/W2237671266","https://openalex.org/W2268491398","https://openalex.org/W2317788533","https://openalex.org/W2473135273","https://openalex.org/W2510841322","https://openalex.org/W2557181747","https://openalex.org/W2563593003","https://openalex.org/W2580171608","https://openalex.org/W2590764628","https://openalex.org/W2595904150","https://openalex.org/W2606439133","https://openalex.org/W2621587306","https://openalex.org/W2624773820","https://openalex.org/W2742894922","https://openalex.org/W2793309516","https://openalex.org/W2889513238","https://openalex.org/W2893054519","https://openalex.org/W2901818893","https://openalex.org/W2906461396","https://openalex.org/W2906655493","https://openalex.org/W2907676659","https://openalex.org/W2920919814","https://openalex.org/W2926667013","https://openalex.org/W2939890479","https://openalex.org/W2952406481","https://openalex.org/W2979549406","https://openalex.org/W2981716740","https://openalex.org/W2994942809","https://openalex.org/W3013504322","https://openalex.org/W3014576393","https://openalex.org/W3034395518","https://openalex.org/W3061328166","https://openalex.org/W3083234002","https://openalex.org/W3084236163","https://openalex.org/W3111023718","https://openalex.org/W3123122710","https://openalex.org/W4206892629","https://openalex.org/W4220765272","https://openalex.org/W4220962256","https://openalex.org/W4239521868","https://openalex.org/W4285395443","https://openalex.org/W4292230674"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W4293199045","https://openalex.org/W2405656580","https://openalex.org/W2642604616","https://openalex.org/W3162049976","https://openalex.org/W4381712632","https://openalex.org/W3163009052","https://openalex.org/W3029656231","https://openalex.org/W4213036952","https://openalex.org/W4377030018"],"abstract_inverted_index":{"The":[0],"critical":[1],"first":[2],"step":[3],"in":[4,43,129],"Clustered":[5],"Regularly":[6],"Interspaced":[7],"Short":[8],"Palindromic":[9],"Repeats":[10],"(CRISPR)-associated":[11],"(CRISPR-Cas)":[12],"protein-mediated":[13],"gene":[14],"editing":[15],"is":[16,41,154,167],"recognizing":[17],"a":[18,59,72,155],"preferred":[19],"protospacer":[20],"adjacent":[21],"motif":[22],"(PAM)":[23],"on":[24],"target":[25],"DNAs":[26],"by":[27],"the":[28,81,97,104,116,123,143],"protein's":[29],"PAM-interacting":[30],"amino":[31],"acids":[32],"(PIAAs).":[33],"Thus,":[34],"accurate":[35],"computational":[36,61],"modeling":[37],"of":[38,74,107,131],"PAM":[39,51],"recognition":[40],"useful":[42,156],"assisting":[44],"CRISPR-Cas":[45,160],"engineering":[46,159],"to":[47,79,103],"relax":[48],"or":[49],"tighten":[50],"requirements":[52],"for":[53,66,84,158],"subsequent":[54],"applications.":[55],"Here,":[56],"we":[57,76],"describe":[58],"universal":[60],"protein":[62],"design":[63],"framework":[64],"(UniDesign)":[65],"designing":[67],"protein-nucleic":[68],"acid":[69],"interactions.":[70],"As":[71],"proof":[73],"concept,":[75],"applied":[77],"UniDesign":[78,140,166],"decode":[80],"PAM-PIAA":[82],"interactions":[83],"eight":[85],"Cas9":[86],"and":[87,127,133,149,161],"two":[88],"Cas12a":[89],"proteins.":[90,110,165],"We":[91],"show":[92],"that,":[93],"given":[94,113],"native":[95,124,150],"PIAAs,":[96,151],"UniDesign-predicted":[98],"PAMs":[99,106,148],"are":[100],"largely":[101,121],"identical":[102],"natural":[105,114,147],"all":[108],"Cas":[109],"In":[111],"turn,":[112],"PAMs,":[115],"computationally":[117],"redesigned":[118],"PIAA":[119],"residues":[120],"recapitulated":[122],"PIAAs":[125],"(74%":[126],"86%":[128],"terms":[130],"identity":[132],"similarity,":[134],"respectively).":[135],"These":[136],"results":[137],"demonstrate":[138],"that":[139],"faithfully":[141],"captures":[142],"mutual":[144],"preference":[145],"between":[146],"suggesting":[152],"it":[153],"tool":[157],"other":[162],"nucleic":[163],"acid-interacting":[164],"open-sourced":[168],"at":[169],"https://github.com/tommyhuangthu/UniDesign.":[170]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2}],"updated_date":"2026-03-26T15:22:09.906841","created_date":"2025-10-10T00:00:00"}
