Protein level predictions 4 - Stability changes prediction

Changes in the stability of the protein as a result of the mutation is one important factors considered to predict the mutations ability to increase disease susceptibility. This subgroup of programs contains tools predicting whether the mutation has an effect on proteins stability.

Programs available

• Auto-Mute
• CUPSAT
• Dmutant
• Eris
• FoldX
• I-Mutant 2.0
• MuPRO
• PoPMuSiC
• SCide
• SCpred
• SRide

An extensive overview of tools predicting protein level changes can be found from the recent review  article by Thusberg and Vihinen. Click here to return to the main page of protein prediction tools.

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Description of programs

Auto-Mute

Auto-Mute is a method server based on Random forest and  Delaunay tesselation of protein structure.  It can obtain up to five snps at the time as an input. 

website: Auto-Mute

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Reference: Masso and Vaisman. Accurate prediction of stability changes in protein mutants by combining machine learning with structure based computational mutagenesis. Bioinformatics, 2008, 24, 18, 2002-2009. doi:10.1093/bioinformatics/btn353

CUPSAT

website: CUPSAT

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Reference: Parthiban et al. CUPSAT: prediction of protein stability upon point mutations.  Nucleic Acids Res., 2006, 34, Web Server issue, W239-42. doi:10.1093/nar/gkl190

Dmutant

website: Dmutant

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Reference: Zhou and Zhou. Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci., 2002, 11, 11, 2714-2726. doi:10.1110/ps.0217002

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Eris

website: Eris

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Reference: Yin et al. Eris: an automated estimator of protein stability.  Nat.Methods, 2007, 4, 6, 466-467. doi:10.1038/nmeth0607-466.

FoldX

website: FoldX

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Reference: Guerois et al. Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J.Mol.Biol., 2002, 320, 2, 369-387. doi:10.1016/S0022-2836(02)00442-4

I-Mutant 2.0

website: I-Mutant 2.0

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References:

• Capriotti et al. Predicting protein stability changes from sequences using support vector machines. Bioinformatics, 2005, 21 Suppl 2, ii54-8. doi:10.1093/bioinformatics/bti1109

• Capriotti et al. I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure. Nucleic Acids Res., 2005, 33, Web Server issue, W306-10. doi:10.1093/nar/gki375

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MuPRO

website: MuPRO

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Reference: Cheng et al. Prediction of protein stability changes for single-site mutations using support vector machines. Proteins, 2006, 62, 4, 1125-1132. doi:10.1002/prot.20810

PoPMuSiC

website: PopMuSiC

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References:

• Gilis and Rooman. PoPMuSiC, an algorithm for predicting protein mutant stability changes: application to prion proteins. Protein Eng., 2000, 13, 12, 849-856. http://peds.oxfordjournals.org/cgi/content/full/13/12/849

• Dehouck et al. Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0. Bioinformatics, 2009, 25, 19, 2537-2543.  doi:10.1093/bioinformatics/btp445

SCide

website: SCide

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Reference: Dosztanyi et al. SCide: identification of stabilization centers in proteins. Bioinformatics, 2003, 19, 7, 899-900.

doi:10.1093/bioinformatics/btg110

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SCpred

website: SCpred

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Reference: Dosztanyi et al. Stabilization centers in proteins: identification, characterization and predictions. J.Mol.Biol., 1997, 272, 4, 597-612. doi:10.1006/jmbi.1997.1242  

SRide

website: SRide

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Reference: Magyar et al. SRide: a server for identifying stabilizing residues in proteins. Nucleic Acids Res., 2005, 33, Web Server issue, W303-5. doi:10.1093/nar/gki409

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Useful databases

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Review articles

• Janita Thusberg and Mauno Vihinen. Pathogenic or Not? And If So, Then How? Studying the Effects of Missense Mutations Using Bioinformatics Methods. Hum Mutat. 2009 May;30(5):703-14: doi:10.1002/humu.20938

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Other articles

• Rainer Winnenburg , Conrad Plake and Michael Schroeder. Improved mutation tagging with gene identifiers applied to membrane protein stability prediction. BMC Bioinformatics 2009, 10(Suppl 8):S3. doi:10.1186/1471-2105-10-S8-S3

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Useful Links

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