Language models enable zero-shot prediction of the effects of mutations on protein function

J Meier, R Rao, R Verkuil, J Liu… - Advances in neural …, 2021 - proceedings.neurips.cc
J Meier, R Rao, R Verkuil, J Liu, T Sercu, A Rives
Advances in neural information processing systems, 2021proceedings.neurips.cc
Modeling the effect of sequence variation on function is a fundamental problem for
understanding and designing proteins. Since evolution encodes information about function
into patterns in protein sequences, unsupervised models of variant effects can be learned
from sequence data. The approach to date has been to fit a model to a family of related
sequences. The conventional setting is limited, since a new model must be trained for each
prediction task. We show that using only zero-shot inference, without any supervision from …
Abstract
Modeling the effect of sequence variation on function is a fundamental problem for understanding and designing proteins. Since evolution encodes information about function into patterns in protein sequences, unsupervised models of variant effects can be learned from sequence data. The approach to date has been to fit a model to a family of related sequences. The conventional setting is limited, since a new model must be trained for each prediction task. We show that using only zero-shot inference, without any supervision from experimental data or additional training, protein language models capture the functional effects of sequence variation, performing at state-of-the-art.
proceedings.neurips.cc
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