Prediction of 3D neighbours of molecular surface patches in proteins by artificial neural networks

MOTIVATION Molecular Surface Patches (MSPs) of proteins are responsible for selective interactions between internal parts of one protein molecule or between protein and other molecules. The prediction of the neighbours of a distinct Secondary Structural Element (SSE) would be an important step for protein structure prediction. RESULTS Based on a computational analysis of complementary molecular patches of SSEs, feed-forward Neural Networks (NNs) are trained on a large set of helices for predicting the neighbours of given MSPs. Accuracy of prediction is 96% if only two types of neighbours: solvent or protein are considered, yet drops to 81% for three types of neighbours: (1) solvent, (2) helix/strand or (3) coil. Implications of the method for the prediction of protein structure and subunit interaction are discussed. As a special test case, the structurally equivalent helices of monomeric myoglobin and the homologous subunits of tetrameric haemoglobin are compared.