Fold recognition by concurrent use of solvent accessibility and residue depth

Recognizing the structural similarity without significant sequence identity (called fold recognition) is the key for bridging the gap between the number of known protein sequences and the number of structures solved. Previously, we developed a fold-recognition method called SP3 which combines sequence-derived sequence profiles, secondary-structure profiles and residue-depth dependent, structure-derived sequence profiles. The use of residue-depth-dependent profiles makes SP3 one of the best automatic predictors in CASP 6. Because residue depth (RD) and solvent accessible surface area (solvent accessibility) are complementary in describing the exposure of a residue to solvent, we test whether or not incorporation Of solvent-accessibility profiles into SP3 could further increase the accuracy of fold recognition. The resulting method, called SP4, was tested in SALIGN benchmark for alignment accuracy and Lindahl, LiveBench 8 and CASP7 blind prediction for fold recognition sensitivity and model-structure accuracy. For remote homologs, SP4 is found to consistently improve over SP3 in the accuracy of sequence alignment and predicted structural models as well as in the sensitivity of fold recognition. Our result suggests that RD and solvent accessibility can be used concurrently for improving the accuracy and sensitivity of fold recognition. The SP4 server and its local usage package are available on http://sparks.informatics.iupui.edu/SP4.