AlphaFold: Highly accurate protein structure prediction for WHO priority pathogens

Dear All,

I learned today from our colleagues at WHO that Alphafold has recently added the proteome of nearly all the WHO priority pathogens to their library of highly accurate prediction of protein structures. Alphafold was new to me and is amazing! Per our colleagues at WHO:

  • AlphaFold is an AI system developed by DeepMind that predicts a protein’s 3D structure from its amino acid sequence.
  • It regularly achieves accuracy competitive with experimental results.
  • DeepMind and EMBL’s European Bioinformatics Institute (EMBL-EBI) have partnered to make these predictions freely available to the scientific community.
  • The database will be expanded during 2022 to cover a large proportion of all catalogued proteins (the over 100 million in UniRef90).


I’ve listed all current proteomes in the AlphaFold database below my signature. The list is very broad and I’ll name just a few to give you the idea: mammals (man, mouse, rat), plants (maize, soybeans), fungi (Candida albicans, Fonsecaea pedrosoi), parasites (Brugia malayi, Trypanosoma brucei), and bacteria (S. aureus, M. tuberculosis).

Truly science at its best … this is a stunning resource! I’ve known about DeepMind and chess (and other games) but being able to predict protein structures without the slow, expensive (and not always even possible for some proteins) process of crystallography would seem to open many, many research avenues. Wow! Many thanks to the teams at DeepMind and EMBL!

All best wishes, –jr

John H. Rex, MD | Chief Medical Officer, F2G Ltd. | Operating Partner, Advent Life Sciences. Follow me on Twitter: @JohnRex_NewAbx. See past newsletters and subscribe for the future: https://amr.solutions/blog/. All opinions are my own.

Current list (alphabetical order)

  1. Ajellomyces capsulatus
  2. Arabidopsis thaliana
  3. Brugia malayi
  4. Caenorhabditis elegans (Nematode worm)
  5. Campylobacter jejuni
  6. Candida albicans
  7. Cladophialophora carrionii
  8. Danio rerio (Zebrafish)
  9. Dictyostelium discoideum
  10. Dracunculus medinensis
  11. Drosophila melanogaster (Fruit fly)
  12. Enterococcus faecium
  13. Escherichia coli
  14. Fonsecaea pedrosoi
  15. Glycine max (Soybean)
  16. Haemophilus influenzae
  17. Helicobacter pylori
  18. Homo sapiens (Human)
  19. Klebsiella pneumoniae
  20. Leishmania infantum
  21. Madurella mycetomatis
  22. Methanocaldococcus jannaschii
  23. Mus musculus (Mouse)
  24. Mycobacterium leprae
  25. Mycobacterium tuberculosis
  26. Mycobacterium ulcerans
  27. Neisseria gonorrhoeae
  28. Nocardia brasiliensis
  29. Onchocerca volvulus
  30. Oryza sativa (Asian rice)
  31. Paracoccidioides lutzii
  32. Plasmodium falciparum
  33. Pseudomonas aeruginosa
  34. Rattus norvegicus (Rat)
  35. Saccharomyces cerevisiae (Budding yeast)
  36. Salmonella typhimurium
  37. Schistosoma mansoni
  38. Schizosaccharomyces pombe (Fission yeast)
  39. Shigella dysenteriae
  40. Sporothrix schenckii
  41. Staphylococcus aureus
  42. Streptococcus pneumoniae
  43. Strongyloides stercoralis
  44. Trichuris trichiura
  45. Trypanosoma brucei
  46. Trypanosoma cruzi
  47. Wuchereria bancrofti
  48. Zea mays (Maize)

Current funding opportunities (most current list is here):

  • The PAR Foundation has two open calls. First, are early career grants (students at bachelor and masters level, PhD students, and individuals graduating during 2020-2022) of up to ~€30k to support 1-year projects on prevention of antibiotic resistance. Second, grants up to ~€1000k to support projects with the potential to prevent infections and antibiotic resistance among elderly. Go here for details; the deadline for both is 10 Mar 2022.
  • NIAID has released a four-pronged BAA (Broad Agency Announcement (HHS-NIH-NIAID-BAA2022-1) that covers therapeutics (antibacterial, antifungal, antiviral), vaccines (again, all 3 areas), and diagnostics. Lots of possibilities! The due date is 18 Mar 2022.
  • BARDA’s RFP to support new antibiotics for Yersinia pestis, Francisella tularensis, Burkholderia pseudomallei is open through 6 April 2022. The RFP offers from funding from LO to Phase 2. Go here for the details.
  • JPIAMR’s 14th call is now open. Entitled “Disrupting drug resistance using innovative design”, the call seeks consortia that would seek to “improve the treatment of bacterial and fungal infections (including co-infection) and/or the prevention of the emergence/spread of resistance in humans, animals or plants through the improvement of the efficacy, specificity, delivery, combinations and/or repurposing of drugs and plant protection agents.” Bacteria, fungi, human health, animal health, and plant health are all in scope! Pre-proposals are due 8 Mar 2022; full proposals would be due 5 July 2022. Go here for details.
  • The AMR Action Fund is now open to proposals for funding of Phase 2 / Phase 3 antibacterial therapeutics. Per its charter, the fund prioritizes investment in treatments that address a pathogen prioritized by the WHO, the CDC and/or other public health entities that: (i) are novel (e.g., absence of known cross-resistance, novel targets, new chemical classes, or new mechanisms of action); and/or (ii) have significant differentiated clinical utility (e.g., differentiated innovation that provides clinical value versus standard of care to prescribers and patients, such as safety/tolerability, oral formulation, different spectrum of activity); and (iii) reduce patient mortality. It is also expected that such agents would have the potential to strongly address the likely requirements for delinked Pull incentives such as the UK (NHS England) subscription pilot and the PASTEUR Act in the US. Submit queries to contact@amractionfund.com.
  • INCATE (Incubator for Antibacterial Therapies in Europe) is a newly launched early-stage funding vehicle. Details are still coming into focus, but per comments on 25 Aug 2021 at the BIOCOM conference, their goal is to support ~4 companies per year with about $250k/company. Contact details are on their website (https://www.incate.net/).
  • CARB-X recently announced that their existing resources will be reserved to fund their existing portfolio (more than 80 total awards, and counting, as they include contracting from prior rounds). New rounds from CARB-X will occur only after new funding is obtained in 2021.
  • It’s not a funder, but AiCuris’ AiCubator offers incubator support to very early stage projects. Read more about it here.
  • The Global AMR R&D Hub’s dynamic dashboard (link) summarizes the global clinical development pipeline, incentives for AMR R&D, and investors/investments in AMR R&D.
  • In addition to the lists provided by the Global AMR R&D Hub, you might also be interested in my most current lists of R&D incentives (link) and priority pathogens (link).


Upcoming meetings of interest to the AMR community (most current list is here):

  • [If you missed it, you can now watch the video] 8 Dec: “The New Winds Pushing and Pulling Antibacterial Development.” This was a GREAT program that featured talks from the UK team behind the NHS “Netflix” pilot, Kevin Outterson’s recently released report documenting the need for global Pull incentives to have a value of $2.2 – 4.8b, and speakers covering PASTEUR and work in the EU on pull incentives. The video is here — please make time to listen to this program!
  • 2-3 Feb 2022 (virtual): 10th Advances Against Aspergillosis and Mucormycosis. Registration closes on 30 Jan 2022. Go here for details.
  • 2-3 Feb 2022 (virtual): Antimicrobial Chemotherapy Virtual Conference jointly organised by GARDP with the British Society for Antimicrobial Chemotherapy (BSAC), Center for Disease Dynamics, Economics & Policy (CDDEP) and the Indian Council of Medical Research (ICMR). Click here for details.
  • 4 Feb 2022 (virtual, 5-6.30p GMT): Launch of the GRAM (Global Research on Antimicrobial Resistance) report. Sponsored by the Institute for Health Metrics and Evaluation, the University of Oxford, the Fleming Fund, the Bill & Melinda Gates Foundation and Wellcome Trust, this report by Murray et al. is based on 471 million individual records or isolates and 7585 study-location-years’ worth of data and shows that at least 1.27 million deaths per year are directly attributable to AMR. Amazing stuff! #AMRSOS! Go here to register. If you miss it, a post-event recording will be available.
  • 7 Feb 2022 (virtual, 10a-11.30a and 3:30p-5p CET): 2-part webinar entitled Antimicrobial Consumption & Use – Data for Action as part of the WHO Global Webinar Series. Be sure to register for both session 1 and session 2
  • 3 Mar 2022 (virtual, 2p GMT): The Longitude Prize (run by Nesta Challenges), CARB-X and FIND, have joined forces for a virtual event in March, AMR& Diagnostic Frontiers: Developing and increasing access to innovative diagnostics in and for low-and-middle-income countries (LMICs). Full agenda details and registration can be found here, including an invitation for diagnostic companies to pitch to a panel of global health representatives.
  • 3-6 Mar 2022 (Albuquerque, New Mexico): Biannual meeting of the MSGERC (Mycoses Study Group Education and Research Consortium). Details are here.
  • 6-11 Mar 2022 (Il Ciocco, Tuscany): Gordon Research Conference entitled “New Antibacterial Discovery and Development”. Go here for details, go here for the linked 5-6 Mar Gordon Research Seminar that precedes it.
  • 9 Mar 2022 (virtual, and in-person): BioInfect Conference, Alderley Park, UK (near Manchester). This long-running Bionow-sponsored annual conference draws a very strong audience. Go here for details.
  • 7-8 Apr 2022 (Basel and in person, we hope): The 6th edition of the annual AMR conference sponsored by the BEAM AllianceCARB-X, the Novo REPAIR Impact Fund, the IMI Accelerator, and the European Biotechnology Network. Go here for the hold-the-date page and a way to be kept informed about the meeting. 
  • 9-13 May 2022 (Athens and online): 40th Annual Meeting of the European Society for Paediatric Infectious Diseases, Go here for details.
  • 20-24 Sep 2022 (New Delhi): 21st Congress of the International Society for Human and Animal Mycology (ISHAM). Go here for details.
  • 25-28 Oct 2022 (Stellenbosch, South Africa): The University of Cape Town’s H3D Research Centre will celebrate its 10th anniversary with a symposium covering the Centre’s research on Malaria, TB, Neglected Tropical Diseases, and AMR. Go here to register.

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