BeEP (after Best Evolutionary Pattern) is a quality assessment method designed to validate protein structural models through an explicit use of evolutionary information. Each structure model under consideration is used to derive a model of protein evolution represented by a set of site-specific substitution matrices that consider the structural constraints of the model. Using maximum likelihood estimations it is possible to correlate the substitution pattern originated from the analyzed model with the information contained in a sequence alignment of homologous proteins. The best structural models are those that provide a better explanation of the evolutionary pattern based on the constraints that modulate sequence divergence.

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   Upload 1 to 15 protein structure files in PDB format, individually or in compressed file(s) (see an example and more information):

   Upload a sequence alignment of your target protein in Phylip format (Optional; see an example and more information):

   Upload a phylogenetic tree related to your alignment in Newick format (Optional; see an example and more information):

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