Papers › Variational auto-encoding of protein sequences
Variational auto-encoding of protein sequences
Sam Sinai, Eric Kelsic, George M. Church, Martin A. Nowak
Proteins are responsible for the most diverse set of functions in biology. The ability to extract information from protein sequences and to predict the effects of mutations is extremely valuable in many domains of biology and medicine. However the mapping between protein sequence and function is complex and poorly understood. Here we present an embedding of natural protein sequences using a Variational Auto-Encoder and use it to predict how mutations affect protein function. We use this unsupervised approach to cluster natural variants and learn interactions between sets of positions within a protein. This approach generally performs better than baseline methods that consider no interactions within sequences, and in some cases better than the state-of-the-art approaches that use the inverse-Potts model. This generative model can be used to computationally guide exploration of protein sequence space and to better inform rational and automatic protein design.
In Syntology View this paper on Syntology: its repositories, every harvested function with whether it ran, its licence and the call to fetch it.
Open this paper in Syntology's Atlas, the map of the papers in Syntology's graph and their citations.
Code
Repository list and official/mentioned flags are the archive's, frozen 2025-07-28. Reachability, where shown, is from one Syntology probe window (2026-09-16 to 2026-09-18); repositories not probed show nothing. GitHub stars are not tracked.
Code Syntology ran Syntology
Not run by Syntology. Nothing on this page verifies that the listed code works.
Tasks
Results from the paper archive 2025-07-28
No leaderboard rows for this paper in the archive.
Report a problem or propose a change · a person checks every report against the paper or source before anything changes; decisions are listed on /corrections