{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Feng H"],"funding":["U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences","U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)","U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)","NHGRI NIH HHS","U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute","NIGMS NIH HHS","NIH HHS"],"pagination":["2279"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC10937933"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["15(1)"],"pubmed_abstract":["UV-crosslinking of protein and RNA in direct contacts has been widely used to study protein-RNA complexes while our understanding of the photo-crosslinking mechanisms remains poor. This knowledge gap is due to the challenge of precisely mapping the crosslink sites in protein and RNA simultaneously in their native sequence and structural contexts. Here we systematically analyze protein-RNA interactions and photo-crosslinking by bridging crosslinked nucleotides and amino acids mapped using different assays with protein-RNA complex structures. We developed a computational method PxR3D-map which reliably predicts crosslink sites using structural information characterizing protein-RNA interaction interfaces. Analysis of the informative features revealed that photo-crosslinking is facilitated by"],"journal":["Nature communications"],"pubmed_title":["Structure-based prediction and characterization of photo-crosslinking in native protein-RNA complexes."],"pmcid":["PMC10937933"],"funding_grant_id":["R03 HG009528","R01 GM096889","R35GM145279","S10 OD012351","R03HG009528","R35 GM145279","R01GM096889","S10 OD021764"],"pubmed_authors":["Rudnick ND","Liu L","Feng H","Maji S","Ustianenko D","Zhang C","Lu XJ"],"additional_accession":[]},"is_claimable":false,"name":"Structure-based prediction and characterization of photo-crosslinking in native protein-RNA complexes.","description":"UV-crosslinking of protein and RNA in direct contacts has been widely used to study protein-RNA complexes while our understanding of the photo-crosslinking mechanisms remains poor. This knowledge gap is due to the challenge of precisely mapping the crosslink sites in protein and RNA simultaneously in their native sequence and structural contexts. Here we systematically analyze protein-RNA interactions and photo-crosslinking by bridging crosslinked nucleotides and amino acids mapped using different assays with protein-RNA complex structures. We developed a computational method PxR3D-map which reliably predicts crosslink sites using structural information characterizing protein-RNA interaction interfaces. Analysis of the informative features revealed that photo-crosslinking is facilitated by","dates":{"release":"2024-01-01T00:00:00Z","publication":"2024 Mar","modification":"2026-07-15T13:29:36.892Z","creation":"2026-07-05T03:08:15.901Z"},"accession":"S-EPMC10937933","cross_references":{"pubmed":["38480694"],"doi":["10.1038/s41467-024-46429-y"]}}