#Structome

Ashar Malik

@proteinmechanic.bsky.social

1 month ago

Like with the MBE work, DeepRoots introduces a new and much faster way to bootstrap. It achieves this by introducing "Embedding Jitter"—injecting Gaussian noise into the latent space to estimate branch support.

#Phylogenetics #StructuralBiology #Structome #Evolution #StructuralPhylogenetics #StrPhy

Ashar Malik

@proteinmechanic.bsky.social

1 month ago

Protein structure is more conserved than sequence. Work in 2020 (MBE: academic.oup.com/mbe/article/...), showed 3D data unlocks deeper evolutionary signals. A thought was why not go higher than 3D? 🧵

#Phylogenetics #StructuralBiology #Structome #Evolution #StructuralPhylogenetics #StrPhy

Ashar Malik

@proteinmechanic.bsky.social

1 year ago

Future work 1) inclusion of custom structure search 2) and I am working on digesting large scale text data via LLMs to offer meaningful text-based insights per query.

Feedback requested:

What would you improve?

#Structome #StructuralPhylogenetics #Science

Ashar Malik

@proteinmechanic.bsky.social

1 year ago

Structome-TM: Complementing dataset assembly for structural phylogenetics by addressing size-based biases The increasing availability of protein structures presents new opportunities for detecting homologous proteins. While global alignment methods are widely used and generally effective, they often strug...

Structome-TM preprint now live @ www.biorxiv.org/content/10.1...

@biorxivpreprint.bsky.social
#Science #Structome #StructuralPhylogenetics

Ashar Malik

@proteinmechanic.bsky.social

1 year ago

#Structome began as an initiative to explore #evolutionary signals from #proteins sharing a structural neighborhood. It uses Q-score to rapidly gather datasets & build NJ trees. To highlight usage of Q-score, the tool is now called Structome-Q. App available here: biosig.lab.uq.edu.au/structome_q/