Protein Structure and Function: Application of Bioinformatics Methods - John Rigden 2014

Prediction of Protein Function Based on Theoretical Models
What's Next?

Despite the utility of protein modeling Methods, the insights they offer into protein function are not accessible to all biologists. Easy access to reliable models provided by various Databases is the first step toward establishing a dialogue between modelers and experimental biologists. The interaction between these two communities is not only mutually beneficial in its own right, but also essential for the effective development of both disciplines. Structural models can significantly facilitate the design and interpretation of wet-lab experiments by narrowing down the number of hypotheses to be tested, and occasionally by providing very precise suggestions for planned experiments. Therefore, we suggest that ongoing efforts to identify yet-unknown Proteins with established enzymatic activities (Roberts 2004) should be integrated with modeling efforts, helping to bridge the gap between the Functions of uncharacterized proteins and the sequences whose functions remain to be predicted.

On the other hand, it should be kept in mind that current function catalogs are limited to experimentally verified annotations. In other words, function prediction typically involves searching for a matching function among already known ones, while hypotheses regarding possible but yet-undescribed functions are rarely proposed. Put differently, there are currently no de novo function prediction methods. Thus, while The Development of such novel computational approaches is encouraging, existing pattern-based methods still rely on experimental support to identify novel reactions and pathways that can subsequently be added to Cell/13.html">Protein Structure and sequence databases. Experimental analysis becomes even more crucial in light of recent findings showing that the discovery rate of new Protein Families remains virtually constant (Yooseph et al. 2007), meaning we are still far from grasping the full extent of the diverse functional space represented by Earth's proteins (Raes et al. 2007).