Enhancing the Protein Tertiary Structure Prediction by Multiple Sequence
  Alignment Generation
Le Zhang Jiayang Chen Tao Shen Yu Li Siqi Sun
The field of protein folding research has been greatly advanced by deep
learning methods, with AlphaFold2 (AF2) demonstrating exceptional performance
and atomic-level precision. As co-evolution is integral to protein structure
prediction, AF2's accuracy is significantly influenced by the depth of multiple
sequence alignment (MSA), which requires extensive exploration of a large
protein database for similar sequences. However, not all protein sequences
possess abundant homologous families, and consequently, AF2's performance can
degrade on such queries, at times failing to produce meaningful results. To
address this, we introduce a novel generative language model, MSA-Augmenter,
which leverages protein-specific attention mechanisms and large-scale MSAs to
generate useful, novel protein sequences not currently found in databases.
These sequences supplement shallow MSAs, enhancing the accuracy of structural
property predictions. Our experiments on CASP14 demonstrate that MSA-Augmenter
can generate de novo sequences that retain co-evolutionary information from
inferior MSAs, thereby improving protein structure prediction quality on top of
strong AF2.