on the day the news came out, I did wonder if the AlphaFold2 team somehow had access to all the preliminary PDB files sent around via Gmail (which belongs to the same company), but more as a joke/conspirational thought. "our" target T1052, was also predicted very well by domains and as a monomer. It will be interesting to see how well future iterations of the method can assemble the complete protein chain and the complete protein chains into the correct heteromer.
Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 Section Editor Acta Crystallographica F https://journals.iucr.org/f/ > On 9 Dec 2020, at 10:37, Cedric Govaerts <cedric.govae...@ulb.ac.be> wrote: > > Dear All > > After about 10 (!) years of (very) hard work we solved the structures of our > dearest membrane transporter. Dataset at 2.9 And resolution, fairly > anisotropic, experimental phasing, and many looooong nights with Coot and > Buster to achieve model refinement. > > The experimental structure had a well defined ligand nicely coordinated but > also a lipid embedded inside the binding cavity (a complete surprise but > biologically relevant) and two detergent molecules well defined > (experimental/crystallisation artefact). > > As our paper was accepted basically when CASP organisers were calling for > targets I offered my baby to the computing Gods. However we only provided the > sequence to CASP, no info regarding any ligand or lipid. > > Less than a month after, the CASP team contacted us and send us the best > model. In fact it was 2 half models as the transporter is a pseudo dimer, > with the N-lobe and C-lobe moving relative to each other during transport > cycle, thus divided as two domains in CASP. > > The results were breathtaking. 0.7 And RSMD on one half, 0.6 on the other. > And yes, group 427 was the superpower (did not know at the time that it was > AlphaFold). > > We had long discussions with the CASP team, as -for us- this almost exact > modelling was dream-like (or science fiction) and -at some point- we were > even suspecting fraud, as our coordinates had travelled over the internet a > few times around when interacting with colleagues. The organisers reassured > us that we were not the only target that had been “nailed” so no reason to > suspect any wrongdoing. > > To this day I am still baffled and I would be happy to hear from the > community, maybe from some of the CASP participants. > > The target is T024, the “perfect" models are domain-split version (T024-D1 > and T024-D2), as AlphaFold2 did not perform so well on the complete assembly. > Deposited PDB is 6T1Z > > Cedric > > PS: I should also note that many other groups performed very well, much > better than I would have dreamed, including on the full protein but just not > as crazy-good. > — > Prof. Cedric Govaerts, Ph.D. > Universite Libre de Bruxelles > Campus Plaine. Phone :+32 2 650 53 77 > Building BC, Room 1C4 203 > Boulevard du Triomphe, Acces 2 > 1050 Brussels > Belgium > http://govaertslab.ulb.ac.be/ <http://govaertslab.ulb.ac.be/> > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> ######################################################################## 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/
