Software

We have developed SCPE (Structurally Constrained Protein Evolutionary model) and PCDB (Protein Conformational Database). Please find more information below.

SCPEv1.2
(Structurally Constrained Protein Evolutionary model)

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The SCPE model was developed by Gustavo Parisi and Julian Echave. It is a program to simulate protein sequence divergence under protein structural constraints.

During evolution, protein structures are more conserved than the sequences encoding for them. The fact that structural databases as CATH and SCOP contain homologous super families with almost identical structures but with no apparent signal of sequential conservation, represents and extreme example of how protein structure conservation constraints sequence divergence.
Recently Maria Silvina Fornasari extended the applicability of SCPE to proteins with quaternary structure. This resides in the fact that the conservation of protein-protein interactions in oligomers imposes additional constraints to sequence divergence.

The main output of an SCPE simulation is a whole set of site-specific substitution matrices, the equilibrium frequencies also site-specific and number of total contacts per site.
To use these site-specific matrices in protein maximum likelihood evolutionary studies, the SCPE prints out input files to be used with the program HYPHY. HYPHY is one of the very few phylogenetic analysis programs that can handle with site-specific substitution matrices. HYPHY can be downloaded from http://www.hyphy.org.

If you use SCPE please cite:

Parisi, G and Echave, J. Structural constraints and emergence of sequence patterns in protein evolution. Molecular Biology and Evolution.18 (5): 750-756, 2001.
Fornasari, MS, Parisi, G and Ecahve, J. Quaternary structure constraints on evolutionary sequence divergence. Fornasari, MS, Parisi, G and Echave, J. In press Molecular Biology and Evolution 2006

PCDB
(Protein Conformational Database)

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PCDB is a database of protein conformational diversity. For each represented domain, the database contains the redundant compilation of all corresponding different crystallographic structures. These structures represent the solved structure of the same domain under different conditions and can be consequently considered as different instances of the protein native fold. As a measure of the conformational diversity we use the RMSD obtained comparing the structures deposited for each domain. The represented domains were extracted from CATH database and afterwards cross linked with additional information from several sources and methods. This database makes possible the study of correlations between the extension of conformational diversity registered in domains and a collection of physicochemical and biological parameters of the polypeptide, such as protein function, presence of ligands, mutations, structural classification, taxonomy, among others.

If you use PCDB please cite:

Juritz E, Fernandez Alberti S, Parisi G. PCDB: A database of protein conformational diversity. Nucleic Acids Research. 2010. Submitted.