Protein metal binding residue prediction based on neural networks

Abstract

It is known that over one-third of protein structures contain metal ions, and they are the necessary elements in life system. Traditionally, structural biologists used to investigate properties of metalloproteins (proteins which bind with metal ions) by physical means and interpret the function formation and reaction mechanism of enzyme by their structures and observation from experiments in vitro. Most of proteins have primary structures (amino acid sequence information) only; however, the 3-dimension structures are not always available. In this paper, a direct analysis method is proposed to predict protein metalbinding amino acid residues only from its sequence information by neural network with sliding window-based feature extraction and biological feature encoding techniques and it can successfully detect 15 binding elements in protein, and 6 binding elements in enzyme.