2°Struc - the Protein Secondary Structure Analysis Server

Abstract

Protein secondary structure can be defined by the pattern of hydrogen bonding between backbone amide and carboxyl groups, whereby the protein is constrained to adopt repetitive dihedral angle conformations. “Define Secondary Structure of Proteins” (DSSP)(Kabsch and Sander, 1983) is the de facto standard for annotation using rules similar to those described by Pauling and Corey, (1951) to assign eight secondary structure states. However, other methods have been developed to address problems including poor edge residue definition, low-resolution structure elucidation and Cα only structures. These methods define secondary structure in different ways resulting in a wide variation in assignment at the amino acid and segment levels. To enable investigation of this variation we present 2°Struc; a web server that analyses protein secondary structure content derived from a number of available methods. The output is in five sections. Protein structure summary details the ‘whole protein’ percentage structure content and provides a numerical comparison of each method relative to DSSP using several commonly applied metrics including percentage similarity and Matthews correlation coefficient. Structure summary by chain displays percentage content and provides an option to compare each structure assignment method using the Jmol molecular viewer. Multiple structure alignment uses a three-state representation colored to display secondary structure assignments relative to PDB and UniProt sequence records for each method. A majority vote consensus is also provided. Original multiple structure alignment provides a second colored alignment displaying unmodified structure assignments. Sequence structure alignments shows comparative unmodified and modified three-state output relative to UniProt and ATOM record sequences, with an option to download a PDF file containing information about the method run, percentage structure content, chain length and diagram of the three-state structure assignment, also provided. (Supported by a grant from the BBSRC Bioinformatics and Biological Resources Fund, UK).