Zhidian Zhang

Hit or Miss: Understanding Emergence and Absence of Homo-oligomeric Contacts in Protein Language Models

This study shows that large protein language models can predict homo-oligomeric interface contacts, with performance improving with model size and alignment diversity.

Scaling down protein language modeling with MSA Pairformer

This paper introduces MSA Pairformer, a memory-efficient protein language model that outperforms existing methods in contact prediction and variant effect prediction.

BoltzDesign1: Inverting All-Atom Structure Prediction Model for Generalized Biomolecular Binder Design

BoltzDesign1 inverts AlphaFold3 to design protein binders for diverse targets without model finetuning, achieving high in silico success rates and structural diversity.

Protein language models learn evolutionary statistics of interacting sequence motifs

The paper investigates how ESM-2, a protein language model, predicts protein contacts by analyzing coevolving residue statistics and local sequence context.

Differential Effects of Posttranslational Modifications on the Membrane Interaction of Huntingtin Protein

This study investigates how posttranslational modifications affect the membrane interaction and helical structure of the N-terminal fragment of the huntingtin protein.