PRESS-PLOT: An Online Server for Protein Structural Analysis and Evaluation with Residue-level Virtual Angle Correlation Plots

Abstract

Based on the data and tools in PRESS, especially the residue-level virtual angle correlation plots, a web-server called PRESS-PLOT is further developed for easy access and display of the plots for structural analysis and evaluation. A structure to be analyzed and evaluated can be submitted to the server by either giving its structural ID in PDB or uploading its structural file in the PDB format. The residue-level virtual bond angles and torsion angles of the structure are then computed. The neighboring virtual bond angle and torsion angle pairs are displayed as scattered points in a 2D graph and compared against the 2D contour map of the density distribution of such angle pairs in known protein structures, as given in the background of the 2D graph. The virtual angle pairs that can be analyzed and evaluated include α-τ and τ-β angle pairs as they appear in either general structures or specific secondary structures such as α-helices, β-sheets, or their turns. As a justification of PRESS-PLOT, more than 1000 obsoleted structures (with lower resolutions) in PDB are evaluated using PRESS-PLOT and compared with their current superseded versions (with higher resolutions). The results show that PRESS-PLOT distinguishes high-quality structures (the current ones) from low-quality structures (the obsoleted ones) clearly in its angle correlation plots. The PRESS-PLOT server can be accessed online at http://pidd.math.iastate.edu/press/ .