Protein level predictions 8 - Other tools predicting protein functional changes

[Description of the   tool set|

Programs available

Proteomic tools

• SABLE
• SNPeffect

Taxonomic tools

• ACCFold (tool predicting protein fold)
  

Other  tools

• ExPASy

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

Proteomics tools

SABLE

[Description  including method used + input +output info]

website: SABLE

Download:

Reference:

SNPeffect

website:SNPeffect

Download:

Reference: Reumers et al. SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs. Nucleic Acids Res., 2005, 33, Database issue, D527-32. doi:10.1093/nar/gki086

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Taxonomic methods

ACCFold

ACCFolde is "a simple and powerful method is presented for taxonomic fold recognition, which combines support vector machine (SVM) with autocross-covariance (ACC) transformation. The evolutionary information represented in the form of position-specific score matrices is converted into a series of fixed-length vectors by ACC transformation and these vectors are then input to a SVM classifier for fold recognition. The sequence-order effect can be effectively captured by this scheme." (citation from Dong et al).

website:

Download: here

Reference: Qiwen Dong, Shuigeng Zhou, Jihong Guan.Protein fold recognition based on auto-cross covariance transformation. Bioinformatics, 2009. doi:10.1093/bioinformatics/btp500

Other tools

ExPASy

ExPASy site contains posttranslational modification prediction tools.

website: ExPASy

Download:

Reference:

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Useful databases

• PDB (database of protein structures containing currently around 60 000 protein structures)
• DMDM (database of domain mapping of disease mutations) 

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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

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Useful Links

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