SPDesign: protein sequence designer based on structural sequence profile using ultrafast shape recognition.

ABSTRACT: Protein sequence design can provide valuable insights into biopharmaceuticals and disease treatments. Currently, most protein sequence design methods based on deep learning focus on network architecture optimization, while ignoring protein-specific physicochemical features. Inspired by the successful application of structure templates and pre-trained models in the protein structure prediction, we explored whether the representation of structural sequence profile can be used for protein sequence design. In this work, we propose SPDesign, a method for protein sequence design based on structural sequence profile using ultrafast shape recognition. Given an input backbone structure, SPDesign utilizes ultrafast shape recognition vectors to accelerate the search for similar protein structures in

SUBMITTER: Wang H 

PROVIDER: S-EPMC11006797 | biostudies-literature | 2024 Mar

REPOSITORIES: biostudies-literature