Thank you to all who replied and for the tip off about the prize - all very newsworthy ;-0 Will try to summarise everything in a para or two. Congrats to the winners!!
Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Sent from Proton Mail Android -------- Original Message -------- On 07/10/2024 16:24, Mark Glover wrote: > We had an interesting case for a protein-RNA structure. We had determined the > first structure of a FinO family RNA chaperone bound to its RNA target. The > structure was deposited in the PDB just after AF3 gathered its training > database so we thought this would be a nice test of AF3 for protein-RNA > prediction. Our structure is stabilized by two main contacts: recognition of > the terminal 3' nucleotide by a hairpin-helix motif in the protein, and > recognition of the RNA hairpin by a novel protein N-cap structure. While the > structure has no homologs in the database, there are structures in the > protein-RNA PDB that do contain those interactions. We ran many different > predictions, and we found that AF3 would generally place the RNA over the > correct surface on the protein, however the detailed interactions were often > wrong. AF3 did get the N-cap interaction in some of the predictions, but > never correctly predicted the recognition of the 3' nucleotide. > Mark > > On Sat, Oct 5, 2024 at 7:49 AM Jon Cooper > <0000488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote: > >> Just wondering if anyone has any comments on, or concrete experiences with, >> alphafold3. I might try to cobble something together for Crystallography >> News (he says, having missed the main Nature paper, ahem). My googling has >> only given me hype and gripe so far ;-0 ;-0 >> >> Best wishes, Jon Cooper. >> jon.b.coo...@protonmail.com >> >> Sent from Proton Mail Android >> >> ######################################################################## >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> >> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing >> list hosted by www.jiscmail.ac.uk, terms & conditions are available at >> https://www.jiscmail.ac.uk/policyandsecurity/ > > -- > > --------------------------------------------- > Mark Glover > Chair, Department of Biochemistry > University of Alberta > Edmonton, AB > T6G 2H7 > office: 780-492-2136 > lab: 780-492-0886 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
