Effect of the sequence data deluge on the performance of methods for detecting protein functional residues

Computational prediction of protein functional sites-Applications in biotechnology and biomedicine

There are many computational approaches for predicting protein functional sites based on different sequence and structural features. These methods are essential to cope with the sequence deluge that is filling databases with uncharacterized protein sequences. They complement the more expensive and time-consuming experimental approaches by pointing them to possible candidate positions. In many cases they are jointly used to characterize the functional sites in proteins of biotechnological and biomedical interest and eventually modify them for different purposes. There is a clear trend towards approaches based on machine learning and those using structural information, due to the recent developments in these areas. Nevertheless, "classic" methods based on sequence and evolutionary features are still playing an important role as these features are strongly related to functionality. In this review, the main approaches for predicting general functional sites in a protein are discussed, with a focus on sequence-based approaches.

Computational methods and tools for binding site recognition between proteins and small molecules: from classical geometrical approaches to modern machine learning strategies

In the current "genomic era" the number of identified genes is growing exponentially. However, the biological function of a large number of the corresponding proteins is still unknown. Recognition of small molecule ligands (e.g., substrates, inhibitors, allosteric regulators, etc.) is pivotal for protein functions in the vast majority of the cases and knowledge of the region where these processes take place is essential for protein function prediction and drug design. In this regard, computational methods represent essential tools to tackle this problem. A significant number of software tools have been developed in the last few years which exploit either protein sequence information, structure information or both. This review describes the most recent developments in protein function recognition and binding site prediction, in terms of both freely-available and commercial solutions and tools, detailing the main characteristics of the considered tools and providing a comparative analysis of their performance.