ResidueFinder: extracting individual residue mentions from protein literature.

ABSTRACT:

Background

The revolution in molecular biology has shown how protein function and structure are based on specific sequences of amino acids. Thus, an important feature in many papers is the mention of the significance of individual amino acids in the context of the entire sequence of the protein. MutationFinder is a widely used program for finding mentions of specific mutations in texts. We report on augmenting the positive attributes of MutationFinder with a more inclusive regular expression list to create ResidueFinder, which finds mentions of native amino acids as well as mutations. We also consider parameter options for both ResidueFinder and MutationFinder to explore trade-offs between precision, recall, and computational efficiency. We test our methods and software in full tex

SUBMITTER: Becker TE 

PROVIDER: S-EPMC8293528 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature