> they can maintain an advantage through several routes - they can > publish in patents (so people can see what they’ve done, but not legally > implement it )
In Europe and I think some other countries, inventions can only be patented if they have *industrial applicability.* In any case, academics all over the world tend to ignore them. On Wed, Dec 9, 2020 at 12:18 PM Harry Powell - CCP4BB < 0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > Hi > > Actually, since Deep Mind is a commercial organization (funded by > shareholders and people who buy their services), I don’t think they are > subject to the same rules as academia as regards making their source code > public. It would be very nice if they would (could?) make their code > public, but I don’t see any obligation to do so. Their responsibility is > primarily to their shareholders (you can argue the rights and wrongs of > that until the cows come home). > > Commercially, they can maintain an advantage through several routes - they > can publish in patents (so people can see what they’ve done, but not > legally implement it without a licence), they can keep it all confidential > and hope that no-one manages to reverse engineer and implement it (at the > risk of someone else publishing the details and removing their advantage), > they can publish something that is honest but just misleading enough (or > lacking in detail) to throw people off the scent, or… > > If they can provoke other developers to work out where they have gone > wrong and produce something that competes with AlphaFold2, that would be > great. If they can provide something like a web service that allows users > to run their method, that would be great too, but the important thing is > (that unless they had prior knowledge of the structures in CASP14) they’ve > done something that no-one else has managed to do as well in spite of years > of trying. > > Just my two ha’porth. > > Harry > > > On 9 Dec 2020, at 10:36, Hughes, Jonathan < > jon.hug...@bot3.bio.uni-giessen.de> wrote: > > > > i think the answer to all these doubts and questions is quite simple: > the AlphaFold2 people must make all details of their methods public (source > code) and, as would probably be necessary, open their system for inspection > and use by independent experts. isn't that what peer review and > reproducibility are all about? those rules date from the time before every > tom, dick and henriette could publicize anything they like inside their own > zuckerberg bubble. my opinion is that this is a virtual infectious disease > that will cause humanity far bigger problems than corona ever will – i just > hope i'm wrong! > > > > best > > > > jon > > > > > > > > Von: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> Im Auftrag von Mark J > van Raaij > > Gesendet: Mittwoch, 9. Dezember 2020 11:14 > > An: CCP4BB@JISCMAIL.AC.UK > > Betreff: Re: [ccp4bb] External: Re: [ccp4bb] AlphaFold: more thinking > and less pipetting (?) > > > > > > > > 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/ > > > > > > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > 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 > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > 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/ > -- patr...@douglas.co.uk Douglas Instruments Ltd. Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK Directors: Patrick Shaw Stewart, Peter Baldock, Stefan Kolek http://www.douglas.co.uk Tel: 44 (0) 148-864-9090 US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36 ######################################################################## 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/
