4 papers
Few-shot Protein Fitness Prediction via In-context Learning and Test-time Training
Felix Teufel, Aaron W. Kollasch, Yining Huang +4
Accurately predicting protein fitness with minimal experimental data is a persistent challenge in protein engineering. We introduce PRIMO (PRotein In-context Mutation Oracle), a tr…
MotifBench: A standardized protein design benchmark for motif-scaffolding problems
Zhuoqi Zheng, Bo Zhang, Kieran Didi +5
The motif-scaffolding problem is a central task in computational protein design: Given the coordinates of atoms in a geometry chosen to confer a desired biochemical function (a mot…
Towards deep learning sequence-structure co-generation for protein design
Chentong Wang, Sarah Alamdari, Carles Domingo-Enrich +2
Deep generative models that learn from the distribution of natural protein sequences and structures may enable the design of new proteins with valuable functions. While the majorit…
EnzymeFlow: Generating Reaction-specific Enzyme Catalytic Pockets through Flow Matching and Co-Evolutionary Dynamics
Chenqing Hua, Yong Liu, Dinghuai Zhang +6
Enzyme design is a critical area in biotechnology, with applications ranging from drug development to synthetic biology. Traditional methods for enzyme function prediction or prote…