PCI-SS: Web-based human and machine interfaces for protein secondary structure prediction

Abstract

PCI-SS is a Web-based protein secondary structure prediction service that makes use of novel dynamic nonlinear system identification techniques. When used to combine multiple prediction systems, PCI-SS exhibits state-of-the-art prediction accuracy while reducing confusion of helix and strand structures, a particularly detrimental class of error, by up to 25%. Unlike other available secondary structure prediction methods, PCI-SS provides both human-readable and machine-readable Web interfaces. In addition to a dynamic PHP-generated Web interface for humans, a Simple Object Access Protocol (SOAP) interface is added to permit invocation of the PCI-SS service remotely. This facilitates incorporation of PCI-SS into systems biology analysis pipelines that require protein secondary structure information, and greatly simplifies high-throughput analyses. WSDL is used to precisely define the SOAP interface. XML is used to represent the input protein sequence data and also to encode the resulting structure prediction in a machine-readable format. To our knowledge, this represents the only publicly available SOAP-interface for a protein secondary structure prediction service.