ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins

Abstract

A major problem in structural biology is the recognition of errors in experimental and theoretical models of protein structures. The ProSA program (Protein Structure Analysis) is an established tool which has a large user base and is frequently employed in the refinement and validation of experimental protein structures and in structure prediction and modeling. The analysis of protein structures is generally a difficult and cumbersome exercise. The new service presented here is a straightforward and easy to use extension of the classic ProSA program which exploits the advantages of interactive web-based applications for the display of scores and energy plots that highlight potential problems spotted in protein structures. In particular, the quality scores of a protein are displayed in the context of all known protein structures and problematic parts of a structure are shown and highlighted in a 3D molecule viewer. The service specifically addresses the needs encountered in the validation of protein structures obtained from X-ray analysis, NMR spectroscopy and theoretical calculations. ProSA-web is accessible at https://prosa.services.came.sbg.ac.at

In silico analysis of Shiga toxins (Stxs) to identify new potential vaccine targets for Shiga toxin-producing Escherichia coli

“…Analysis of the 3D models was made using protein structure analysis (ProSa) server (https://prosa.services.came.sbg.ac.at/prosa.php) (Wiederstein and Sippl 2007) and Ramachandran Plot Analysis resource (RAMPAGE) (Lovell et al 2002). The Z-score (overall model quality) and energy plots were created by ProSa server.…”

Molecular characterization, modeling, in silico analysis of equine pituitary gonadotropin alpha subunit and docking interaction studies with ganirelix

“…The model generated was evaluated in terms of Ramachandran plot, main and side chain parameters and residue properties by PROCHECK (Laskowski et al 1993), Z-score and QMEAN score. The 3D homology model was checked by Procheck and assessed by web servers such as ProSA-Web (Wiederstein and Sippl 2007) and QMEAN (Benkert et al 2009) for model quality estimation. To assess the quality of model, QMEAN Z-score overall quality factor was used and QMEAN score for density plot was used to assess the organization of various atoms.…”

Targeting the ubiquitin-conjugating enzyme E2D4 for cancer drug discovery–a structure-based approach

“…In the minimization process, the bond orders are assigned, hydrogens are added to all the atoms in the system and the water molecules are removed. The refined and energy minimized UBE2D4 model is validated using PROCHECK [34,35], ProSA [36,37] and VERIFY_3D [38,39] server tools. The model is validated for the stereochemical quality, local model quality and overall model quality.…”

“…Stereochemical quality of the energy minimized and refined 3D structure of the UBE2D4 was analysed by Ramachandran plot in PROCHECK server [35]. The Ramachandran contour plot provides the phi (Φ) versus psi (ψ) angles of amino acid residues which form the backbone of the protein and their stereochemical quality [36]. The plot statistics indicate that 91.9% of the residues are present in the most favoured regions, 6.5% of the residues in the additional allowed regions, 0.8% residues in the generously allowed regions and 0.8% of the residues in the disallowed region (Fig.…”