Lucas Tafur @structureltp

Scientist. Personal account. Madrid, Spain Joined September 2022

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Kelvin Lau 🧬🧪💎 @klausenhauser

2 days ago

Always good to remember that the PDB sequence of a structure is not always the sequence of the protein made nor the sequence of the protein analyzed, its the sequence of the protein a human remembered to type in.

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Lucas Tafur @structureltp

3 days ago

@raphaels7 @CocaCola Yeah that’s not a very good reasoning.

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Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social @RolandDunbrack

6 days ago

STOP using ipTM for AlphaFold PPI screens. * Artificially LOW when both full-length proteins have irrelevant, non-binding IDRs or domains. * If one protein is folded & the other contains irrelevant IDRs or domains, the score is too HIGH because of d0. * Use ipSAE or LIS.

Biology+AI Daily @BiologyAIDaily

6 days ago

AF Cache: Efficient Pipeline for Running AlphaFold for High-Throughput Protein-Protein Interaction Prediction 1 AF Cache is a Nextflow pipeline designed to make large-scale protein–protein interaction (PPI) screening practical with AlphaFold2 and AlphaFold3 by cutting the

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Lucas Tafur @structureltp

5 days ago

Sooner, rather than later, the AI tech bro startup biotech industry will burst…

Chris Masterjohn @ChrisMasterjohn

5 days ago

This is how you know tech bros are not going to solve major problems in biology.

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James Olzmann @OlzmannLab

a week ago

Exciting new work from @RobertoZoncu, led by all star first authors @clairegoul and @aakritijain24 reveals the mechanism mediating the sensing of lysosomal damage and recruitment of ESCRT for membrane repair. Beautiful work!🤩 nature.com/articles/s4158…

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Ethan J. Weiss @ethanjweiss

a year ago

Just when you think this nonsense can't get any worse, you find this hilarious attempt to lie about the lie: - we made a mistake and did not include the pre-registered primary endpoint when we full-well knew and then attempted to obscure the data and did not include it any of our social media tsunami in early April, nor was it even discussed in the paper, but in this video we admit we had it but just did not like it - but then people went crazy so - we are crafting a story that we were naive and really never should have made this the primary endpoint and actually we really have another way to do this that was the primary methodology (WTF) and should have been the primary endpoint - and now we will spin on and on about how the Cleerly results are just implausibly bad and so must be wrong even though we never even discussed this for one second in our social or in the actual paper - and also it was probably covid or "some covid-related activity" that led to these Cleerly results being so messed up - also here are new data with another method (keep re-analysing it till it looks right) and these data look less bad so it's all good... Seriously, i thought this was a clown show but now I am searching for something that more accurately describes it. I am not sure I can solve that

Dr Gary McGowan @drgarymcgowan

a year ago

KETO-CTA: Schrödinger's Plaque 🥓 In his latest lecture, @realDaveFeldman claims plaque progression was TOO RAPID to make sense. Yet, we were told "NO or MINIMAL plaque progression". Can progression be so great as to not make sense AND also "no or minimal"?

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Nature Aging @NatureAging

2 weeks ago

Online now!✨Iiams, Skinner et al explore the effect of early-onset, lifelong time-restricted feeding in >500 male and female mice, and report extended healthspan in male and female mice, and extended lifespan in male mice @SamIiamsClever @CircadianClocks nature.com/articles/s4358…

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Lucas Tafur @structureltp

2 weeks ago

@ketosavage “X food” fasting is, almost every time a stupid idea.

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Ali H. Shaib @AliHShaib

2 weeks ago

Hello world, meet 1,000× Expansion Microscopy. 1,000,000,000× expansion by volume! A gel that starts at a few centimeters will then expand to the volume of an Olympic swimming pool. biorxiv.org/content/10.648… In our new bioRxiv preprint, work carried out between MIT and UMG, led by Helena Hu in collaboration with scientists from the labs of @eboyden3 Ed Boyden, Silvio Rizzoli, and myself, we present Thousandfold Expansion Microscopy. By enlarging biological specimens across multiple rounds of expansion, molecular-scale features, as small as the distances between adjacent amino acids, can be visualized with conventional optical microscopes. Democratizing super-resolution microscopy.

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Lucas Tafur @structureltp

2 weeks ago

@Brady_H 😭😭I have a pretty good idea who the target public is…

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Alejandro Montenegro @aemonten

2 weeks ago

The reviewers are us

Andrew Leduc @_AndrewLeduc

2 weeks ago

Im not sure I will ever overcome how furious I get reading reviewer comments. You spend 3 years of your life working on something just for 3 people to skim your paper and point out a few things that were already well explained in an incredibly rude way and then reject it

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Marcus Goncalves @MarcusDGon

2 weeks ago

New publication from our group: what happens inside human endometrial tumors during a ketogenic diet? We analyzed paired tumor biopsies before and after a very low-carbohydrate intervention in women with endometrial cancer 🧵

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Lucas Tafur @structureltp

3 weeks ago

@caloriesproper2 Exactly why there are a million runners and saturated marathons but comparably not a lot of weightlifters/powerlifters. Because the former is harder. 🤣

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Lucas Tafur @structureltp

4 weeks ago

@Alexleaf @caloriesproper2 To truly test the PFT you’d have to show at least a correlation between ectopic fat and T2DM burden, negatively but also positively within weight regain contexts.

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Lucas Tafur @structureltp

4 weeks ago

@Alexleaf @caloriesproper2 What one can conclude from the ReTUNE trial is that when people lose fat, some resolve T2DM. Nothing more. The PFT is unfalsifiable because any null result can always be explained by “needs to lose more fat”.

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Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social @RolandDunbrack

4 weeks ago

MD simulations of proteins have been around for almost 50 years (1977). What are you talking about?

Yang Fan 范阳 @Yang_Supertramp

4 weeks ago

For the past 70 years, modern biology has been built on a static objects worldview: DNA = information, proteins = structures, cells = nanomachines, disease = broken parts, drugs = part repair/update. I'm honestly excited for a “new worldview” and “Dynamic Biology” to emerge.

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Lucas Tafur @structureltp

4 weeks ago

@caloriesproper2 Is anyone in academic circles, besides Taylor, who endorses/promotes the PFT?

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Lucas Tafur @structureltp

4 weeks ago

@Alexleaf @caloriesproper2 Not really. If someone loses fat but fails to resolve T2DM, then she/he’s still within his PFT. If she/he does resolve it, then he’s below his PFT. Unfalsifiable. It’s always posthoc because, contrary to energy balance, you cannot model/predict it.