Homology-based inference sets the bar high for protein function prediction.

Background: Any method that de novo predicts protein function should do better than random. More challenging, it also ought to outperform simple homology-based inference.

Methods: Here, we describe a few methods that predict protein function exclusively through homology.

A large-scale evaluation of computational protein function prediction.

Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If computational predictions are to be relied upon, it is crucial that the accuracy of these methods be high.

Disease-related mutations predicted to impact protein function.

Background: Non-synonymous single nucleotide polymorphisms (nsSNPs) alter the protein sequence and can cause disease. The impact has been described by reliable experiments for relatively few mutations. Here, we study predictions for functional impact of disease-annotated mutations from OMIM, PMD and Swiss-Prot and of variants not linked to disease.