Shihao Feng

SoftAlign is an end-to-end protein structure alignment method that improves accuracy over existing tools while being compatible with other alignment strategies.

This paper introduces ProTokens, artificial amino-acid tokens that enable efficient compression and processing of protein structures for design and analysis.

ColabDock improves protein-protein docking by integrating experimental restraints into a framework that outperforms existing methods in complex structure prediction.

This paper introduces a method for efficient de novo protein design using a relaxed sequence space approach, demonstrating successful experimental production of over 50 proteins with desired structural properties.

This paper introduces EGNA, an empirical graph neural network for predicting protein-ligand binding affinity, showing improved accuracy over existing methods on benchmark datasets.

This paper introduces a spectral regularizer to disentangle entropy from coevolution in sequence models, improving interpretability and reducing overfitting in contact map inference.