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

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

2007 | Markus Wiederstein and Manfred J. Sippl*
ProSA-web is an interactive web service designed to assist in the recognition of errors in three-dimensional (3D) protein structures. It is an extension of the widely used ProSA program, which is commonly employed for refining and validating experimental protein structures and for structure prediction and modeling. ProSA-web leverages the advantages of web-based applications to display scores and energy plots, highlighting potential issues in protein structures. The service specifically addresses the validation of protein structures obtained from X-ray analysis, NMR spectroscopy, and theoretical calculations. Users can input atomic coordinates in PDB format or by entering a protein structure code. The service calculates a z-score and provides an energy plot to identify problematic regions, which are then visualized in a 3D molecule viewer. An example using two ABC transporter structures (MsBα and Sav1866) demonstrates how ProSA-web can reveal errors in experimental structures by comparing them to known structures in the Protein Data Bank (PDB). The tool is accessible at https://prosa.services.came.sbg.ac.at.ProSA-web is an interactive web service designed to assist in the recognition of errors in three-dimensional (3D) protein structures. It is an extension of the widely used ProSA program, which is commonly employed for refining and validating experimental protein structures and for structure prediction and modeling. ProSA-web leverages the advantages of web-based applications to display scores and energy plots, highlighting potential issues in protein structures. The service specifically addresses the validation of protein structures obtained from X-ray analysis, NMR spectroscopy, and theoretical calculations. Users can input atomic coordinates in PDB format or by entering a protein structure code. The service calculates a z-score and provides an energy plot to identify problematic regions, which are then visualized in a 3D molecule viewer. An example using two ABC transporter structures (MsBα and Sav1866) demonstrates how ProSA-web can reveal errors in experimental structures by comparing them to known structures in the Protein Data Bank (PDB). The tool is accessible at https://prosa.services.came.sbg.ac.at.
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