ISPRED4: interaction sites PREDiction in protein structures with a refining grammar model

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Abstract

Motivation:

The identification of protein-protein interaction (PPI) sites is an important step towards the characterization of protein functional integration in the cell complexity. Experimental methods are costly and time-consuming and computational tools for predicting PPI sites can fill the gaps of PPI present knowledge.

Results:

We present ISPRED4, an improved structure-based predictor of PPI sites on unbound monomer surfaces. ISPRED4 relies on machine-learning methods and it incorporates features extracted from protein sequence and structure. Cross-validation experiments are carried out on a new dataset that includes 151 high-resolution protein complexes and indicate that ISPRED4 achieves a per-residue Matthew Correlation Coefficient of 0.48 and an overall accuracy of 0.85. Benchmarking results show that ISPRED4 is one of the top-performing PPI site predictors developed so far.

Contact:

gigi@biocomp.unibo.it

Availability and Implementation:

ISPRED4 and datasets used in this study are available at http://ispred4.biocomp.unibo.it.

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