Protein level predictions 8 - Other tools predicting protein functional changes
[Description of the tool set|
[Description including method used + input +output info]
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
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).
Reference: Qiwen Dong, Shuigeng Zhou, Jihong Guan.Protein fold recognition based on auto-cross covariance transformation. Bioinformatics, 2009. doi:10.1093/bioinformatics/btp500
ExPASy site contains posttranslational modification prediction tools.
- PDB (database of protein structures containing currently around 60 000 protein structures)
- DMDM (database of domain mapping of disease mutations)
- 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