Abstract
In recent years, improvements in protein function prediction methods have led to increased success in annotating protein sequences. However, the functions of over 30% of protein-coding genes remain unknown for many sequenced genomes. Protein functions vary widely, from catalyzing chemical reactions to binding DNA or RNA or forming structures in the cell, and some types of functions are challenging to predict due to the physical features associated with those functions. Other complications in understanding protein functions arise due to the fact that many proteins have more than one function or very small differences in sequence or structure that correspond to different functions. We will discuss some of the recent developments in predicting protein functions and some of the remaining challenges.