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09:51
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins
Markus Wiederstein1, Manfred J Sippl
1Center of Applied Molecular Engineering, Division of Bioinformatics, University of Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria.
Nucleic Acids Research
|May 23, 2007
Summary
ProSA-web offers an easy-to-use online tool for identifying errors in protein structures. It visualizes quality scores and highlights problematic regions in 3D, aiding structural biology research.
Area of Science:
- Structural biology
- Computational biology
- Biophysics
Background:
- Recognizing errors in protein structure models is a significant challenge in structural biology.
- The ProSA program (Protein Structure Analysis) is a widely used tool for refining and validating protein structures.
- Analyzing protein structures can be complex and time-consuming.
Purpose of the Study:
- To present ProSA-web, an interactive web-based extension of the ProSA program.
- To simplify the process of identifying and visualizing potential errors in protein structures.
- To provide a user-friendly service for validating protein models from various sources.
Main Methods:
- Developed an interactive web application extending the ProSA program.
- Integrated interactive displays for quality scores and energy plots.
- Implemented a 3D molecule viewer to highlight problematic structural regions.
- Benchmarked quality scores against a database of known protein structures.
Main Results:
- ProSA-web provides straightforward visualization of protein structure quality scores.
- Problematic regions within protein structures are clearly highlighted in a 3D viewer.
- The service facilitates the validation of protein structures from X-ray crystallography, NMR spectroscopy, and theoretical calculations.
- Quality scores are presented in the context of all known protein structures for comparison.
Conclusions:
- ProSA-web enhances the accessibility and ease of protein structure validation.
- The interactive visualization aids in the rapid identification of potential model errors.
- This tool supports researchers in structural biology, biophysics, and computational biology.
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The primary structure of a protein is its amino acid sequence.
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