Hepatitis C virus contact map prediction based on binary encoding strategy

Inter-residue contact map is an important two-dimensional representation of protein spatial structure, and has much potential application in the area of understanding protein fold mechanism. In the present note, a 19-bit binary input encoding strategy, integrating with residue pair conformational features (possible residue pairwise, residue classification, secondary structure, sequence length, and sequence separation information), is proposed for the purpose of capturing mapping relationship of protein sequence. Simulation results on a set of 61 hepatitis C virus (HCV) retrieved from the protein data bank (PDB) demonstrate that the proposed encoding scheme could precisely capture conformational patterns within HCV protein sequence. This promising result could provide some useful insights into the nature of HCV protein fold mechanism.