Enzymes can be engineered at the level of their amino acid sequences to optimize key
properties such as expression, stability, substrate range, and catalytic efficiency─ or even to …

Microbes were the only form of life on Earth for most of its history, and they still account for
the vast majority of life's diversity. They convert rocks to soil, produce much of the oxygen we …

Prediction methods inputting embeddings from protein language models have reached or
even surpassed state-of-the-art performance on many protein prediction tasks. In natural …

Protein engineering often targets binding pockets or active sites which are enriched in
epistasis—nonadditive interactions between amino acid substitutions—and where the …

There are more ways to synthesize a 100-amino acid (aa) protein (20100) than there are
atoms in the universe. Only a very small fraction of such a vast sequence space can ever be …

We present MoCHI, a tool to fit interpretable models using deep mutational scanning data.
MoCHI infers free energy changes, as well as interaction terms (energetic couplings) for …

A protein's genetic architecture–the set of causal rules by which its sequence produces its
functions–also determines its possible evolutionary trajectories. Prior research has …

The engineering of novel protein–ligand binding interactions, particularly for complex drug-
like molecules, is an unsolved problem, which could enable many practical applications of …

Paralogous genes are often functionally redundant for long periods of time. While their
functions are preserved, paralogs accumulate cryptic changes in sequence and expression …

Antibodies are engineerable quantities in medicine. Learning antibody molecular
recognition would enable the in silico design of high affinity binders against nearly any …