In a single long MD simulation we saw a loop change from a closed (red) to open (green) state, with many short "false openings" (yellow). In this pre-print, we characterize the loop residues that act as a conformational switch, and see that the motif occurs in other proteins too

If you are looking for antibiotic summary cards:

MIT Intro to Deep Learning - 2023 Lectures are Live MIT Intro to Deep Learning is one of few concise deep learning courses on the web. The course quickly takes you to the foundations of deep learning, neural net architectures, and applications of DL. introtodeeplearning.com

And, hAMRonization 2.0 workshop is happening now 😃 Su Datt Lam Ang Mia Yang Sabrina Di Gregorio Emma Griffiths Finlay Mclintock Public Health Alliance for Genomic Epidemiology Zetty giving opening remarks:

And it's a wrap!! Thank you for coming! 😍🌷 Many thanks to Su Datt Lam Ang Mia Yang Sabrina Di Gregorio zetty and Prof Sheila Nathan, Emma Griffiths Finlay Mclintock Public Health Alliance for Genomic Epidemiology

What is an exon??? New paper w/ Dr. Edward Wallace and julie aspden in Cell Genomics : cell.com/cell-genomics/… Cue 🧵1/8

PICKLUSTER: A protein-interface clustering and analysis plug-in for UCSF ChimeraX biorxiv.org/cgi/content/sh… #biorxiv_bioinfo

The human genome is gradually unravelling its secrets 🎁 AlphaMissense model Science Magazine: one more path lit up by deep learning in exploring the code of life 🧬 We now know with high confidence if 89% of ALL missense variants are benign or pathogenic Key contributions🧵🧵

Want to know what a single-residue substitution does to your favorite protein? Together with @TobiasRaisch we wrote a tool to easily visualize pathogenicity scores from the Google DeepMind #AlphaMissense paper: github.com/MPI-Dortmund/p… We hope you find it interesting :-)

ChatGPT can now browse the internet to provide you with current and authoritative information, complete with direct links to sources. It is no longer limited to data before September 2021.

Are there any privileged routes of acquisition of #driver alterations in #cancer? Can they be used to #predict the outcome of treatments at diagnosis? In our latest work, out in Nature Communications, we show that such routes do exist for most cancer types! nature.com/articles/s4146… 1/6

Ligand docking is a key component in comp drug discovery. AF-latest outperforms classical systems like AutoDock Vina on the PoseBusters benchmark. This is despite baselines having access to the ground-truth protein structure information that AlphaFold-latest doesn’t get. 4/7

Thrilled to announce AlphaFold 3 which can predict the structures and interactions of nearly all of life’s molecules with state-of-the-art accuracy including proteins, DNA and RNA. Biology is a complex dynamical system so modeling interactions is crucial blog.google/technology/ai/…

#AlphaFold3 is out, and good gravy is it a read. Congrats to the Google DeepMind Isomorphic Labs folks, some seriously compelling results especially for antibody-antigen complex predictions. Has got me thinking a lot!

AF3 server is LIVE! Just tried predicting complex with almost 5K amino acids. TIP: you need to click "continue with google" to access the server (otherwise the "server" is grayed out). alphafoldserver.com

Automated molecular optimization of a BRD4 inhibitor using #AlphaFold predicted structure with our new #GenerativeAI drug design method, DrugHIVE. paper: pubs.acs.org/doi/10.1021/ac… GitHub: github.com/jssweller/Drug… Remo Rohs lab USC Dept. of Quantitative & Computational Biology. JCIM & JCTC Journals. #compchem #machinelearning

Modeling protein-small molecule conformational ensembles with ChemNet Institute for Protein Design 🚀 New preprint from David Baker!🚀 - ChemNet is a breakthrough deep learning model that accurately predicts the conformational ensembles of small molecules in complex with proteins. - It

Have you ever wanted to design protein binders with ease? Today we present 𝑩𝒊𝒏𝒅𝑪𝒓𝒂𝒇𝒕, a user-friendly and open-source pipeline that allows to anyone to create protein binders de novo with high experimental success rates. Bruno Correia Sergey Ovchinnikov biorxiv.org/content/10.110…

Best Practices for Using AI When Writing Scientific Manuscripts (1/3)

Trained in #AMR wet-lab, doing #AMR genome sequencing, but wrangling with bioinformatics coding which is never really your thing? Fret not, AMRColab is here for you! 1) We compiled #AMR analysis (AMRFinderPlus, ResFinder), comparison (hAMRonization) into a GoogleColab - 1/n