Protein Contact Order Prediction: Update

Contact order (CO) is the most widely used approach to quantitatively measure the topological complexity of protein structures. CO can be used to accurately predict protein folding rates and to assist in de novo protein structure prediction/ generation. However, the utility of the CO method, especially for experimentalists, has been limited by the lack of availability of programs or web servers that either support CO calculation or allow CO prediction. For proteins with solved three-dimensional structures, the authors have developed a public web server that accurately calculates COs, thereby overcoming the limited functionality of an earlier web server. In addition, this server also offers a very effective method for predicting protein contact order from primary sequence data. Many factors, in particular the percentage of residues in alpha helices, the percentage of residues in beta strands, and sequence length, are known to be strongly correlated with the absolute contact order.