Jul 20, 2019

FunFam protein families improve residue level molecular function prediction

BMC Bioinformatics
Linus ScheibenreifBurkhard Rost

Abstract

The CATH database provides a hierarchical classification of protein domain structures including a sub-classification of superfamilies into functional families (FunFams). We analyzed the similarity of binding site annotations in these FunFams and incorporated FunFams into the prediction of protein binding residues. FunFam members agreed, on average, in 36.9 ± 0.6% of their binding residue annotations. This constituted a 6.7-fold increase over randomly grouped proteins and a 1.2-fold increase (1.1-fold on the same dataset) over proteins with the same enzymatic function (identical Enzyme Commission, EC, number). Mapping de novo binding residue prediction methods (BindPredict-CCS, BindPredict-CC) onto FunFam resulted in consensus predictions for those residues that were aligned and predicted alike (binding/non-binding) within a FunFam. This simple consensus increased the F1-score (for binding) 1.5-fold over the original prediction method. Variation of the threshold for how many proteins in the consensus prediction had to agree provided a convenient control of accuracy/precision and coverage/recall, e.g. reaching a precision as high as 60.8 ± 0.4% for a stringent threshold. The FunFams outperformed even the carefully curated EC numb...Continue Reading

Mentioned in this Paper

Protein Binding
Classification
Gene Products, Protein
Molecular_function
Plasma Protein Binding Capacity
Site
Binding (Molecular Function)
Protein Domain
Structure
Protein Structure Databases

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