A High Performing Tool for Residue Solvent Accessibility Prediction

Abstract

Abstract. Many efforts were spent in the last years in bridging the gap between the huge number of sequenced proteins and the relatively few solved structures. Relative Solvent Accessibility (RSA) prediction of residues in protein complexes is a key step towards secondary structure and protein-protein interaction sites prediction. With very different approaches, a number of software tools for RSA prediction have been produced throughout the last twenty years. Here, we present a binary classifier which implements a new method mainly based on sequence homology and implemented by means of look-up tables. The tool exploits residue similarity in solvent exposure pattern of neighboring context in similar protein chains, using BLAST search and DSSP structure. A two-state classification with 89.5% accuracy and 0.79 correlation coefficient against the real data is achieved on a widely used dataset.

Deep Autoencoders for Additional Insight into Protein Dynamics

“…In addition to the previously mentioned representation based on angles, we investigate whether enhancing the structural alphabet states (represented by the three angles) with relative solvent accessibility information might bring further insight into the matter at hand. Relative solvent accessibility (RSA) of amino acid residues is a value indicating the degree to which the residue is exposed [20], being able to characterize the spatial distribution of amino acids in a folded protein. RSA is significant for predicting protein-interaction sites [20] and it is used in protein family classification [1].…”

“…Relative solvent accessibility (RSA) of amino acid residues is a value indicating the degree to which the residue is exposed [20], being able to characterize the spatial distribution of amino acids in a folded protein. RSA is significant for predicting protein-interaction sites [20] and it is used in protein family classification [1]. The intuition is that, even if RSA values independently do not offer a unique characterization of a protein, being individually non-specific, new structural states defined by the three angles together with RSA values could bring additional information.…”