Alp Tartici

Inverse FoldDir designs protein sequences compatible with a given backbone structure, achieving high accuracy and experimental validation in nanobody redesign.

This paper identifies High Attention (HA) sites in protein sequences using the ESM model to improve protein family classification and function prediction.

This paper introduces PARSE, a method for protein functional site annotation using local structure embeddings, achieving high accuracy in predicting catalytic residues and novel functions.

The paper uses self-supervised deep learning to cluster local 3D protein structures, creating a motif lexicon that improves structure prediction, drug off-target prediction, and variant analysis.

Pool PaRTI improves protein sequence representations by using PageRank on transformer attention matrices to identify critical residues, enhancing performance and interpretability across ML tasks.

This study shows that metabolic defects in C. elegans lead to hyperactive mitochondria and Parkinson's-like traits, with metformin improving motor function and reducing neurodegeneration.