Hi Tom, Great to see your new analysis and publication. A wonderful addition to your recent work in this domain/comparisons. Congratulations!
For those trying to keep up with "AI Drug Discovery" (including AlphaFold, OpenFold, Gen AI, etc) vs "Conventional Drug Discovery" (primarily crystallography/CryoEM/structural biology/biophysics for this audience), a few recent papers and news items: "AI’s potential to accelerate drug discovery needs a reality check" https://www.nature.com/articles/d41586-023-03172-6 "Sumitomo Schizophrenia Drug Discovered With AI Tech Fails in Two Phase 3 Trials" https://medcitynews.com/2023/07/sumitomo-schizophrenia-ai-drug-discovery-in-two-clinical-trial/ "AI-created drugs fall off hype cycle" https://www.beckershospitalreview.com/pharmacy/ai-created-drugs-fall-off-hype-cycle.html "After years of hype, the first AI-designed drugs fall short in the clinic" https://endpts.com/first-ai-designed-drugs-fall-short-in-the-clinic-following-years-of-hype/ As a research community, while it is great to see new sci & tech maturing and adding to the R&D, it's quite likely that when the dust settles (as we've seen with many hypes, I think there are ~200 companies of different sizes and stages claiming to be in the "AI" space, most with undisclosed and unvalidated methods and approaches), all this could become a strong *addition* to the drug discovery/structural biology arsenal, *instead of substituting workhorse solutions and approaches*, potentially *most useful in cases only when experimental structures are not available or not immediately possible to kick off the start of projects*. Best regards, Debanu -- Debanu Das, https://bio.site/debanu_das On Fri, Dec 1, 2023 at 10:23 AM Mitchell D. Miller < mitchell.d.mil...@rice.edu> wrote: > The Baker group has also reported substantial progress in all atom > predictions > > Krishna et al., > Generalized Biomolecular Modeling and Design with RoseTTAFold All-Atom > bioRxiv 2023.10.09.561603 > doi: 10.1101/2023.10.09.561603 > https://www.biorxiv.org/content/10.1101/2023.10.09.561603v1.full > > Regards, > Mitch > > Quoting Tom Terwilliger <0000b6116340b489-dmarc-requ...@jiscmail.ac.uk>: > > > Hi Roberto, > > Thanks for the link to the DeepMind site! I hadn't seen that and now I > > read it and the paper that they link to. It looks to me as though they > are > > making significant progress on ligands, dna, rna, but that the program is > > not yet available, so I don't think it can be tested yet! > > All the best, > > Tom T > > > > > > On Fri, Dec 1, 2023 at 5:19 AM Roberto Steiner < > roberto.stei...@kcl.ac.uk> > > wrote: > > > >> Great paper indeed! > >> > >> However quite significant progress seems to have been achieved with > >> ligands as well (and not only)… > >> > >> > https://urldefense.com/v3/__https://deepmind.google/discover/blog/a-glimpse-of-the-next-generation-of-alphafold/__;!!BuQPrrmRaQ!mWTLfJ8Bjj3YYdp1ZCa8HXyjF-1lq1emf12VPcusoqMN5sh4Eajgq-3UOcaWAERlTNpVWXSdqVPUzhyjIYzPrkIn0P-gtdIjb9GM9FxbyWs$ > >> Has anyone in the community put this to the test? > >> > >> > >> Best wishes > >> Roberto > >> > >> > >> *Roberto A Steiner* > >> > https://urldefense.com/v3/__http://www.steinerlab.org__;!!BuQPrrmRaQ!mWTLfJ8Bjj3YYdp1ZCa8HXyjF-1lq1emf12VPcusoqMN5sh4Eajgq-3UOcaWAERlTNpVWXSdqVPUzhyjIYzPrkIn0P-gtdIjb9GMxbA8Qgg$ > >> > https://urldefense.com/v3/__https://twitter.com/steiner_lab__;!!BuQPrrmRaQ!mWTLfJ8Bjj3YYdp1ZCa8HXyjF-1lq1emf12VPcusoqMN5sh4Eajgq-3UOcaWAERlTNpVWXSdqVPUzhyjIYzPrkIn0P-gtdIjb9GMZmS2rX0$ > >> > >> roberto.stei...@kcl.ac.uk > >> Randall Centre for Cell and Molecular Biophysics > >> Faculty of Life Sciences and Medicine > >> King's College London > >> Room 3.10A > >> New Hunt's House, Guy's Campus > >> SE1 1UL, London, UK > >> Phone 0044 20 78488216 > >> Fax 0044 20 78486435 > >> > >> roberto.stei...@unipd.it > >> Dipartimento di Scienze Biomediche > >> Università degli Studi di Padova > >> Viale G. Colombo 3 > >> 35131 Padova, Italia > >> Telefono 0039 049 8276409 > >> > >> *Responses to emails are not expected outside of your normal working > >> hours.* > >> > >> > >> > >> > >> > >> > >> > >> > >> On 30 Nov 2023, at 22:35, Tom Terwilliger < > >> 0000b6116340b489-dmarc-requ...@jiscmail.ac.uk> wrote: > >> > >> You don't often get email from > >> 0000b6116340b489-dmarc-requ...@jiscmail.ac.uk. Learn why this is > important > >> <https://aka.ms/LearnAboutSenderIdentification> > >> Hi Structural biologist colleagues! > >> > >> Our article that helps you make the case that the experiment is still > very > >> much needed is now out: > >> > >> https://www.nature.com/articles/s41592-023-02087-4 > >> > >> "AlphaFold predictions are valuable hypotheses and accelerate but do not > >> replace experimental structure determination." Nature Methods (2023) > >> > >> Also, here is a video on the Phenix Tutorials YouTube channel that > >> describes this analysis: > >> > https://urldefense.com/v3/__https://www.youtube.com/watch?v=ugMPYdPo8Bc__;!!BuQPrrmRaQ!mWTLfJ8Bjj3YYdp1ZCa8HXyjF-1lq1emf12VPcusoqMN5sh4Eajgq-3UOcaWAERlTNpVWXSdqVPUzhyjIYzPrkIn0P-gtdIjb9GMqp4wPP4$ > >> > >> (I hope you will be happy to see that you and your structural biology > >> colleagues get the credit for making AlphaFold possible at 2:35 in the > >> introduction of this video! Keep up the fantastic structural biology > work!) > >> > >> All the best, > >> Tom T > >> -- > >> Thomas C Terwilliger > >> Laboratory Fellow, Los Alamos National Laboratory > >> Senior Scientist, New Mexico Consortium > >> 100 Entrada Dr, Los Alamos, NM 87544 > >> Email: tterwilli...@newmexicoconsortium.org > >> Tel: 505-431-0010 > >> > >> > >> ------------------------------ > >> > >> To unsubscribe from the CCP4BB list, click the following link: > >> > https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!BuQPrrmRaQ!mWTLfJ8Bjj3YYdp1ZCa8HXyjF-1lq1emf12VPcusoqMN5sh4Eajgq-3UOcaWAERlTNpVWXSdqVPUzhyjIYzPrkIn0P-gtdIjb9GMTS3GjrY$ > >> > >> > >> > > > > -- > > Thomas C Terwilliger > > Laboratory Fellow, Los Alamos National Laboratory > > Senior Scientist, New Mexico Consortium > > 100 Entrada Dr, Los Alamos, NM 87544 > > Email: tterwilli...@newmexicoconsortium.org > > Tel: 505-431-0010 > > > > ######################################################################## > > > > To unsubscribe from the CCP4BB list, click the following link: > > > https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!BuQPrrmRaQ!mWTLfJ8Bjj3YYdp1ZCa8HXyjF-1lq1emf12VPcusoqMN5sh4Eajgq-3UOcaWAERlTNpVWXSdqVPUzhyjIYzPrkIn0P-gtdIjb9GMTS3GjrY$ > > > > This message was issued to members of > > > https://urldefense.com/v3/__http://www.jiscmail.ac.uk/CCP4BB__;!!BuQPrrmRaQ!mWTLfJ8Bjj3YYdp1ZCa8HXyjF-1lq1emf12VPcusoqMN5sh4Eajgq-3UOcaWAERlTNpVWXSdqVPUzhyjIYzPrkIn0P-gtdIjb9GM6b0LSR0$ > , a mailing list hosted by > https://urldefense.com/v3/__http://www.jiscmail.ac.uk__;!!BuQPrrmRaQ!mWTLfJ8Bjj3YYdp1ZCa8HXyjF-1lq1emf12VPcusoqMN5sh4Eajgq-3UOcaWAERlTNpVWXSdqVPUzhyjIYzPrkIn0P-gtdIjb9GMrJES6CY$ > , terms & conditions are available at > > > https://urldefense.com/v3/__https://www.jiscmail.ac.uk/policyandsecurity/__;!!BuQPrrmRaQ!mWTLfJ8Bjj3YYdp1ZCa8HXyjF-1lq1emf12VPcusoqMN5sh4Eajgq-3UOcaWAERlTNpVWXSdqVPUzhyjIYzPrkIn0P-gtdIjb9GM_4rhs78$ > > ######################################################################## > > 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/ > ######################################################################## 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/
