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. 2009 Jan;37(Database issue):D374-9.
doi: 10.1093/nar/gkn704. Epub 2008 Oct 22.

SPROUTS: A Database for the Evaluation of Protein Stability Upon Point Mutation

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Free PMC article

SPROUTS: A Database for the Evaluation of Protein Stability Upon Point Mutation

Mathieu Lonquety et al. Nucleic Acids Res. .
Free PMC article

Abstract

SPROUTS (Structural Prediction for pRotein fOlding UTility System) is a new database that provides access to various structural data sets and integrated functionalities not yet available to the community. The originality of the SPROUTS database is the ability to gain access to a variety of structural analyses at one place and with a strong interaction between them. SPROUTS currently combines data pertaining to 429 structures that capture representative folds and results related to the prediction of critical residues expected to belong to the folding nucleus: the MIR (Most Interacting Residues), the description of the structures in terms of modular fragments: the TEF (Tightened End Fragments), and the calculation at each position of the free energy change gradient upon mutation by one of the 19 amino acids. All database results can be displayed and downloaded in textual files and Excel spreadsheets and visualized on the protein structure. SPROUTS is a unique resource to access as well as visualize state-of-the-art characteristics of protein folding and analyse the effect of point mutations on protein structure. It is available at http://bioinformatics.eas.asu.edu/sprouts.html.

Figures

Figure 1.
Figure 1.
Query interface of SPROUTS with 1gmp as selected structure and default options.
Figure 2.
Figure 2.
Results obtained with the 2D and 3D visualization modes for the 1gmp structure. On the upper window, the graphs correspond to smoothed stability scores along the whole sequence for the DFIRE and I–Mutant sequence + structure tools. The TEF assignment and MIR prediction are also represented below these graphs. The lower window contains a view of the 1gmp structure with the Jmol applet. The stability score for each amino acid is represented by a small sphere whose colour goes from red to blue corresponding to a score in the range of –19 to + 19. The MIR prediction is symbolized by semi–transparent purple spheres on the designated residues and the TEF assignment is characterized by the different colours on the cartoon representation.

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