@article {519,
	title = {SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants.},
	journal = {Nucleic Acids Res},
	volume = {40},
	year = {2012},
	month = {2012 Jan},
	pages = {D935-9},
	abstract = {<p>Single nucleotide variants (SNVs) are, together with copy number variation, the primary source of variation in the human genome and are associated with phenotypic variation such as altered response to drug treatment and susceptibility to disease. Linking structural effects of non-synonymous SNVs to functional outcomes is a major issue in structural bioinformatics. The SNPeffect database (http://snpeffect.switchlab.org) uses sequence- and structure-based bioinformatics tools to predict the effect of protein-coding SNVs on the structural phenotype of proteins. It integrates aggregation prediction (TANGO), amyloid prediction (WALTZ), chaperone-binding prediction (LIMBO) and protein stability analysis (FoldX) for structural phenotyping. Additionally, SNPeffect holds information on affected catalytic sites and a number of post-translational modifications. The database contains all known human protein variants from UniProt, but users can now also submit custom protein variants for a SNPeffect analysis, including automated structure modeling. The new meta-analysis application allows plotting correlations between phenotypic features for a user-selected set of variants.</p>},
	keywords = {Databases, Protein, Humans, Internet, Meta-Analysis as Topic, Phenotype, Polymorphism, Single Nucleotide, Protein Conformation, Proteins},
	issn = {1362-4962},
	doi = {10.1093/nar/gkr996},
	author = {De Baets, Greet and Van Durme, Joost and Reumers, Joke and Maurer-Stroh, Sebastian and Vanhee, Peter and Dopazo, Joaquin and Schymkowitz, Joost and Rousseau, Frederic}
}
@article {21731483,
	title = {An evolutionary trade-off between protein turnover rate and protein aggregation favors a higher aggregation propensity in fast degrading proteins.},
	journal = {PLoS computational biology},
	volume = {7},
	year = {2011},
	month = {2011 Jun},
	pages = {e1002090},
	abstract = {<p>We previously showed the existence of selective pressure against protein aggregation by the enrichment of aggregation-opposing {\textquoteright}gatekeeper{\textquoteright} residues at strategic places along the sequence of proteins. Here we analyzed the relationship between protein lifetime and protein aggregation by combining experimentally determined turnover rates, expression data, structural data and chaperone interaction data on a set of more than 500 proteins. We find that selective pressure on protein sequences against aggregation is not homogeneous but that short-living proteins on average have a higher aggregation propensity and fewer chaperone interactions than long-living proteins. We also find that short-living proteins are more often associated to deposition diseases. These findings suggest that the efficient degradation of high-turnover proteins is sufficient to preclude aggregation, but also that factors that inhibit proteasomal activity, such as physiological ageing, will primarily affect the aggregation of short-living proteins.</p>},
	doi = {10.1371/journal.pcbi.1002090},
	author = {De Baets, Greet and Reumers, Joke and Delgado Blanco, Javier and Dopazo, Joaquin and Schymkowitz, Joost and Rousseau, Frederic}
}
