Senior Bioinformatician @PDBeurope | Working with macromolecular complexes and RNA. Exploring AI, tech, and the intersection of biology and computing

Cambridge, UK
Joined May 2011
In 1971, the landmark meeting “Structure and Function of Proteins at the Three Dimensional Level.” was held at Cold Spring Harbor Laboratory. It provided a venue for ongoing conversations about what it would mean for all scientists to have access to the structural data 1/4
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Sri Devan Appasamy retweeted
We’re pleased to announce #RNAcentral Release 28, bringing together more than 58 million #noncoding #RNA sequences, around 3 million more than in the previous release. For more details: blog.rnacentral.org
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Scientists have mapped in unprecedented detail the proteins that make up the mitochondria in six organisms spanning the eukaryotic tree of life go.nature.com/3WcPDyy
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Check the preprint of our exciting collaboration with @PilarCossio2 and others: Quantifying RNA Folding Equilibria from Unclassfied Cryo-EM Images biorxiv.org/content/10.64898… see Pilar's very nice description. Congrats Deb Maji and team!
1/5 Cryo-EM gives high-resolution RNA structures, but only when high Mg²⁺ freezes out their motion. At physiological conditions, RNAs are dynamic and 3D reconstruction fails. Can we still learn their folding equilibria? New preprint: yes, straight from the raw particle images👇
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Linus Pauling is the only person to have received two unshared Nobel Prizes - in chemistry and peace. He used quantum mechanics to understand and describe chemical bonding. Later he campaigned vehemently against nuclear weapons and spearheaded a petition to ban nuclear testing.
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“This reflects on the really courageous people who joined me in this project when really no respectable conservative physicist would have joined me, but many talented people did and that’s why I’m here”, said Francis Halzen go.nature.com/4hHBlgn
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The cellular landscape of druggable RNA-binding proteins nature.com/articles/s41573-0… rdcu.be/Xdw8gA2w82Ea This new Perspective by @TzelepisLab et al. discusses opportunities to therapeutically target RNA-binding proteins, which are involved in the development of multiple diseases
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I always believed in free education. I made a decision to never monetise my popular UBC and Oxford lectures. I’ve lived my life by working to bring knowledge to everyone on Earth: the pioneering lectures, the startups past and new, and my AI research. This desire came as the result of witnessing and experiencing a lot of suffering in my childhood. This course is part of my legacy and I’m very proud of it, and thankful to Oxford, the TAs and my students then.
My friend works at Anthropic. He said they pay $650,000 a year for people who truly understand deep learning. This exact course by Nando de Freitas is free forever. Most AI courses charge $2,000+ for this foundation. This one is completely free. You get the real technical foundation ➜ taught at Oxford by a professor who later joined DeepMind. Save this ⭣
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Perfection ✨
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Same predicted complex, different confidence scores: ipTM: 0.38 ipSAE: 0.75 Why can these metrics differ? Full breakdown 👇 youtu.be/k4yBqddtPyQ #AlphaFold #AFDB
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Sri Devan Appasamy retweeted
RNA molecules perform remarkably diverse roles in biology. Accurately predicting RNA structure from sequence promises to accelerate understanding of RNA mechanisms and the design of synthetic RNA medicines and devices. However, RNA structure prediction has proven to be a formidable problem. In a new Science study, researchers report an important assessment of state-of-the-art deep learning methods developed toward this goal. Learn more in a new #SciencePerspective: scim.ag/4h3lr0J
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Requiring biomedical PhD students to write a dissertation before graduation is outdated - I think that establishing a preprint/publication requirement in lieu of a dissertation is better for students and better for the scientific community.
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Sri Devan Appasamy retweeted
Today we remember chemistry laureate Ada Yonath who passed away yesterday at the age of 87. At the beginning of the twentieth century, the chemical foundations for life were a mystery. Today we know how many of the most important processes function, all the way down to the atomic level. This is due in part to the work of biochemist, Ada Yonath. In the 1970s, Yonath began a project that culminated in 2000 with her successful mapping (together with other researchers) of the structure of ribosomes – the cell’s own protein factory – by using x-ray crystallography. Among other applications, this has been important in the production of antibiotics. In 2009, Yonath shared the Nobel Prize in Chemistry with Venkatraman Ramakrishnan and Thomas Steitz for studies of the structure and function of the ribosome. Read more: bit.ly/4kJscDU
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New @ScienceMagazine When generative AI enablesRNA design of pseudoknots Heading in the direction of AlphaFold for predicting proteins, but RNA structure is far more intricate science.org/doi/10.1126/scie…
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