A Novel Index of Contact Frequency from Noise Protein –Protein Interaction Data Help for Accurate Interface Residue Pair Prediction

AbstractProtein –protein interactions are important for most biological processes and have been studied for decades. However, the detailed formation mechanism of protein–protein interaction interface is still ambiguous, which makes it difficult to accurately predict the protein–protein interaction interface r esidue pairs. Here, we extract the interface residue–residue contacts from the decoys in the ZDOCK protein–protein complex decoy set with RMSD mostly larger than 3 Å. To accurately compute the interface residue–residue contacts, we define a new constant called interface residue pairs frequen cy, which counts the atom contact numbers between two interface residues. We normalize interface residue pairs frequency to pick out the top residue–residue pairs from all the possible pairs preferential to be on correct protein–protein interaction interface. When tested on 37 protein dimers fro m the decoy set where most decoys are incorrect, our method successfully predicts 30 protein dimers with a success rate of up to 81.1%. Higher accuracy than some other state-of-the-art methods confirmed the performance of our method.

Source: Interdisciplinary Sciences, Computational Life Sciences - March 16, 2020 Category: Bioinformatics Source Type: research