{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Huang X"],"funding":["University of Michigan","Cystic Fibrosis Foundation","NHLBI NIH HHS","National Institutes of Health","NIGMS NIH HHS"],"pagination":["bbad133"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC10199764"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["24(3)"],"pubmed_abstract":["The critical first step in Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated (CRISPR-Cas) protein-mediated gene editing is recognizing a preferred protospacer adjacent motif (PAM) on target DNAs by the protein's PAM-interacting amino acids (PIAAs). Thus, accurate computational modeling of PAM recognition is useful in assisting CRISPR-Cas engineering to relax or tighten PAM requirements for subsequent applications. Here, we describe a universal computational protein design framework (UniDesign) for designing protein-nucleic acid interactions. As a proof of concept, we applied UniDesign to decode the PAM-PIAA interactions for eight Cas9 and two Cas12a proteins. We show that, given native PIAAs, the UniDesign-predicted PAMs are largely identical to the natural PAMs"],"journal":["Briefings in bioinformatics"],"pubmed_title":["Decoding CRISPR-Cas PAM recognition with UniDesign."],"pmcid":["PMC10199764"],"funding_grant_id":["R41 GM122181","R01 HL147527","HL159871","R01 HL159900","R42 GM122181","XU19XX0","GM122181","R01 HL159871","HL147527","HL159900","R41 GM149016","GM149016"],"pubmed_authors":["Xia X","Zhang J","Chen YE","Huang X","Yang D","Xu J","Zhou J"],"additional_accession":[]},"is_claimable":false,"name":"Decoding CRISPR-Cas PAM recognition with UniDesign.","description":"The critical first step in Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated (CRISPR-Cas) protein-mediated gene editing is recognizing a preferred protospacer adjacent motif (PAM) on target DNAs by the protein's PAM-interacting amino acids (PIAAs). Thus, accurate computational modeling of PAM recognition is useful in assisting CRISPR-Cas engineering to relax or tighten PAM requirements for subsequent applications. Here, we describe a universal computational protein design framework (UniDesign) for designing protein-nucleic acid interactions. As a proof of concept, we applied UniDesign to decode the PAM-PIAA interactions for eight Cas9 and two Cas12a proteins. We show that, given native PIAAs, the UniDesign-predicted PAMs are largely identical to the natural PAMs","dates":{"release":"2023-01-01T00:00:00Z","publication":"2023 May","modification":"2026-06-01T21:19:41.461Z","creation":"2025-06-27T03:05:16.757Z"},"accession":"S-EPMC10199764","cross_references":{"pubmed":["37078688"],"doi":["10.1093/bib/bbad133"]}}