ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins
Open accessAbstract
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.
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The quality of the final homology models was assessed using PROCHECK and ProSA.
“The quality of the final models was assessed using PROCHECK56, that provides information about the stereochemical quality, and by the ProSA validation method57 that evaluates model accuracy and statistical significance with a knowledge-based potential.”
From Modeling the binding of diverse ligands within the Ah receptor ligand binding domain (2019) · cites this paper as [57]
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- Authors
- Wiederstein, M., & Sippl, M. J.
- Affiliations
- University of Salzburg (AT)
- Corresponding author
- Sippl, M. J.
- ORCID
- Wiederstein, M.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2007-05-08
- Volume
- 35
- Issue
- Web Server
- Pages
- W407-W410
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC1933241
- OpenAlex
- W1992192767
- Cited by
- 5,909
- References
- 19
- Citations by year
- 2026: 388 · 2025: 572 · 2024: 542 · 2023: 567 · 2022: 589 · 2021: 552 · 2020: 490 · 2019: 341 · 2018: 326 · 2017: 262 · 2016: 240 · 2015: 205 · 2014: 214 · 2013: 171 · 2012: 150
- FWCI
- 30.04
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by-nc
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Funders
- Austrian Science Fund
- Universität Salzburg
- Topics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- PROSA, protein structure validation, web services, interactive 3D visualization, quality scores, X-ray crystallography, NMR spectroscopy, structure refinement, structure prediction
- MeSH terms
- Escherichia coli, Models, Molecular, Molecular Conformation, Protein Conformation, Protein Denaturation, Proteins, Quality Control, Sequence Analysis, Protein Folding, Computational Biology, Internet, Databases, Protein
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