The letter may have had (or helped have) an impact already: On X today from Pushmeet Kohli @ DeepMind
"We love the excitement & results from the community on AlphaFold 3 and are doubling the AF Server daily job limit to 20. Happy to also share that we're working on releasing the AF3 model (incl weights) for academic use, which doesn’t depend on our research infra, within 6 months". > On May 13, 2024, at 11:11 AM, Wankowicz, Stephanie > <0000d0e1738c7100-dmarc-requ...@jiscmail.ac.uk> wrote: > > If it does what it claims – incredibly impressive. The issue we have is there > is no way to verify or validate the claims it is making. > > The letter is a call and start of a conversation about how the ever-changing > landscape of communication and publication of science should be. > > -Stephanie Wankowicz > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK > <mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Krieger, James M > <krieg...@pitt.edu <mailto:krieg...@pitt.edu>> > Sent: Monday, May 13, 2024 10:22 AM > To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> > <CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>> > Subject: Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility > > This Message Is From an External Sender > This message came from outside your organization. > It definitely is impressive but it also has clear limitations > >> On 13 May 2024, at 15:22, Sylvia Fanucchi >> <0000d0c4e77ae410-dmarc-requ...@jiscmail.ac.uk> wrote: >> >> >> You don't often get email from >> 0000d0c4e77ae410-dmarc-requ...@jiscmail.ac.uk. Learn why this is important >> <https://urldefense.com/v3/__https://aka.ms/LearnAboutSenderIdentification__;!!LQC6Cpwp!ojUwuRRzsCarUF-wwnVWIQtQbTonf10zBas4dHDOMDcNF3qWUSO99i3QLLB39nBZ8NEnc9RG_drv9T5at5d7AmVluUFn$> >> >> Is it just me who is really impressed by it? Am I missing something? >> >> Get Outlook for Android >> <https://urldefense.com/v3/__https://aka.ms/AAb9ysg__;!!LQC6Cpwp!ojUwuRRzsCarUF-wwnVWIQtQbTonf10zBas4dHDOMDcNF3qWUSO99i3QLLB39nBZ8NEnc9RG_drv9T5at5d7ArXNQatL$> >> From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Rafael >> Marques <rafael_mmsi...@hotmail.com> >> Sent: Monday, May 13, 2024 3:13:16 PM >> To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> >> Subject: Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility >> >> I tried it yesterday and I was really shocked by how fast it is. When I was >> preparing to submit my second job, the first one was already finished, which >> made me think that I was definitely doing something wrong. Probably I was... >> >> Best wishes >> >> Rafael Marques >> >> >> On 13 May 2024 09:53, Harry Powell >> <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: >> Hi folks >> >> This arrived in my inbox this morning, and I believe that it may provoke >> some discussion… >> >> Wikipedia tells me: στέργει γὰρ οὐδεὶς ἄγγελον κακῶν ἐπῶν >> >> Best wishes! >> >> Harry >> >> > From: Stephanie Wankowicz <mullane.stepha...@gmail.com> >> > Sent: Saturday, May 11, 2024 3:31 PM >> > To: James Fraser <jaimefra...@gmail.com>; Pedro Beltrao >> > <pedrobelt...@gmail.com>; Benjamin Cravatt <crav...@scripps.edu>; Roland >> > Dunbrack <roland.dunbr...@gmail.com>; Anthony Gitter >> > <git...@biostat.wisc.edu>; Kresten Lindorff-Larsen <lindo...@bio.ku.dk>; >> > Sergey Ovchinnikov <s...@mit.edu>; Polizzi, Nicholas F. >> > <nicholasf_poli...@dfci.harvard.edu>; Brian Shoichet <bshoic...@gmail.com> >> > Subject: AlphaFold3 Transparency and Reproducibility >> > >> > >> > This email from mullane.stepha...@gmail.com originates from outside >> > Imperial. Do not click on links and attachments unless you recognise the >> > sender. If you trust the sender, add them to your safe senders list >> > <https://spam.ic.ac.uk/SpamConsole/Senders.aspx> >> > <https://urldefense.com/v3/__https://spam.ic.ac.uk/SpamConsole/Senders.aspx*3E__;JQ!!LQC6Cpwp!ojUwuRRzsCarUF-wwnVWIQtQbTonf10zBas4dHDOMDcNF3qWUSO99i3QLLB39nBZ8NEnc9RG_drv9T5at5d7AkQKssvO$> >> > to disable email stamping for this address. >> > >> > Hello, >> > >> > >> > As many of you, we were incredibly disappointed with the lack of code >> > or even executables accompanying the publication of AlphaFold3 in Nature. >> > AlphaFold3 was released without the means to test and use the software in >> > a high-throughput manner. This does not align with the principles of >> > scientific research, which rely on the ability of the community to >> > evaluate, use, and build upon existing work. >> > >> > >> > >> > We have written a letter, which will be posted on Zenodo and submitted >> > as a Letter to the Editor in the coming days. >> > >> > >> > >> > Please see the entire letter here. >> > <https://docs.google.com/forms/d/e/1FAIpQLSf6ioZPbxiDZy5h4qxo-bHa0XOTOxEYHObht0SX8EgwfPHY_g/viewform?usp=sf_link> >> > >> > <https://urldefense.com/v3/__https://docs.google.com/forms/d/e/1FAIpQLSf6ioZPbxiDZy5h4qxo-bHa0XOTOxEYHObht0SX8EgwfPHY_g/viewform?usp=sf_link*3E__;JQ!!LQC6Cpwp!ojUwuRRzsCarUF-wwnVWIQtQbTonf10zBas4dHDOMDcNF3qWUSO99i3QLLB39nBZ8NEnc9RG_drv9T5at5d7AqTp0-CX$> >> > If you want to endorse this letter, please fill out your name, >> > affiliation, and email in the form. >> > >> > >> > >> > Additionally, a PDF version of the letter can be found here >> > <https://drive.google.com/file/d/1u1D3KzsllpI_6I0drA9RdIiENd9EK1Hz/view?usp=sharing> >> > >> > <https://urldefense.com/v3/__https://drive.google.com/file/d/1u1D3KzsllpI_6I0drA9RdIiENd9EK1Hz/view?usp=sharing*3E__;JQ!!LQC6Cpwp!ojUwuRRzsCarUF-wwnVWIQtQbTonf10zBas4dHDOMDcNF3qWUSO99i3QLLB39nBZ8NEnc9RG_drv9T5at5d7AmjNPgIH$>. >> > >> > >> > >> > Thank you, >> > >> > >> > >> > Stephanie Wankowicz, UCSF >> > >> > Pedro Beltrao, ETH >> > Benjamin Cravatt, Scripps >> > Roland Dunbrack, FCCC >> > Anthony Gitter, UW Madison >> > Kresten Lindorff-Larsen, Copenhagen >> > Sergey Ovchinnikov, MIT >> > Nicholas Polizzi, DFCI/HMS >> > Brian Shoichet, UCSF >> > James Fraser, UCSF >> > >> > >> >> ######################################################################## >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> <https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!LQC6Cpwp!ojUwuRRzsCarUF-wwnVWIQtQbTonf10zBas4dHDOMDcNF3qWUSO99i3QLLB39nBZ8NEnc9RG_drv9T5at5d7AoA8pumq$> >> >> This message was issued to members of www.jiscmail.ac.uk/CCP4BB >> <https://urldefense.com/v3/__http://www.jiscmail.ac.uk/CCP4BB__;!!LQC6Cpwp!ojUwuRRzsCarUF-wwnVWIQtQbTonf10zBas4dHDOMDcNF3qWUSO99i3QLLB39nBZ8NEnc9RG_drv9T5at5d7AgFZZaeK$>, >> a mailing list hosted by www.jiscmail.ac.uk >> <https://urldefense.com/v3/__http://www.jiscmail.ac.uk__;!!LQC6Cpwp!ojUwuRRzsCarUF-wwnVWIQtQbTonf10zBas4dHDOMDcNF3qWUSO99i3QLLB39nBZ8NEnc9RG_drv9T5at5d7An7YNOzL$>, >> terms & conditions are available at >> https://www.jiscmail.ac.uk/policyandsecurity/ >> <https://urldefense.com/v3/__https://www.jiscmail.ac.uk/policyandsecurity/__;!!LQC6Cpwp!ojUwuRRzsCarUF-wwnVWIQtQbTonf10zBas4dHDOMDcNF3qWUSO99i3QLLB39nBZ8NEnc9RG_drv9T5at5d7ApCXqJeM$> >> >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> <https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!LQC6Cpwp!ojUwuRRzsCarUF-wwnVWIQtQbTonf10zBas4dHDOMDcNF3qWUSO99i3QLLB39nBZ8NEnc9RG_drv9T5at5d7AoA8pumq$> >> This communication is intended for the addressee only. It is confidential. >> If you have received this communication in error, please notify us >> immediately and destroy the original message. You may not copy or >> disseminate this communication without the permission of the University. >> Only authorised signatories are competent to enter into agreements on behalf >> of the University and recipients are thus advised that the content of this >> message may not be legally binding on the University and may contain the >> personal views and opinions of the author, which are not necessarily the >> views and opinions of The University of the Witwatersrand, Johannesburg. All >> agreements between the University and outsiders are subject to South African >> Law unless the University agrees in writing to the contrary. >> >> 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://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!LQC6Cpwp!ojUwuRRzsCarUF-wwnVWIQtQbTonf10zBas4dHDOMDcNF3qWUSO99i3QLLB39nBZ8NEnc9RG_drv9T5at5d7AoA8pumq$> > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > <https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!LQC6Cpwp!ojUwuRRzsCarUF-wwnVWIQtQbTonf10zBas4dHDOMDcNF3qWUSO99i3QLLB39nBZ8NEnc9RG_drv9T5at5d7AoA8pumq$> > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, UC Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, UC Berkeley (http://compbiochem.berkeley.edu) Building 91, Room 410 Building 978, Room 4126 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: 0000-0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 91R0183 Berkeley, CA 94720, USA. Executive Assistant: Michael Espinosa [ meespin...@lbl.gov ][ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ ashleyd...@lbl.gov ][ 1-510-486-5455 ] -- ######################################################################## 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/
