Databases
CoDNaS
(Conformational diversity of Native State database)
CoDNaS is a protein conformational database based on proteins derived from PDB. For each represented protein, the database contains the redundant collection of all the corresponding different structures. These structures represent the solved structure of that protein under different conditions and can be consequently considered as different instances of the protein dynamism (conformers). As a measure of protein conformational diversity (PCD) we use the RMSD obtained comparing all the structures deposited for each protein. This database aims to help understanding how the extension of conformational diversity is related with protein function, structural folds and even with sequence divergence during evolution.
Protmiscuity
Promiscuous Proteins Database
ProtMiscuity is a database of catalytic promiscuous proteins obtained through the implementation of web-scraping, text-mining and manual curation over more than 500 scientific publications. ProtMiscuity provides a useful protein dataset for exploring the relationship between protein structure and function, while helping in the discovery of putative catalytic activities or substrates and the development of new predictions tools.
CoDNaS-RNA
Conformational Diversity in the Native State of RNAs
CoDNaS-RNA is a database of the Conformational Diversity in the Native State of RNA molecules. Each entry in CoDNaS-RNA is a redundant collection of known structures of the same RNA molecule, which can be considered as alternative instances of the RNA structure in its native ensemble. The conformers are taken from the wwPDB and include structures solved by X-ray diffraction, Nuclear Magnetic Resonance and cryo-electron microscopy. CoDNaS-RNA allows you to quantify the conformational diversity of a given RNA, compare the structures of selected conformers, retrieve site-specific interactions between RNA and bound polynucleotides or proteins, and get more data cross-referenced from external resources like RNAcentral.
CoDNaS-Q
Conformational Diversity of Native State - Quaternary
CoDNaS Quaternary is a database of Conformational Diversity of Native State in proteins that present a biologically relevant quaternary structure, that collects a high-quality set of homo-oligomeric conformers obtained from the Protein Data Bank (PDB). CoDNaS Quaternary possess a collection of redundant complexes experimentally determined by X-Ray crystallography technique, including their experimental conditions (ligands, pH, temperature, etc), general information (PDB ID, length, etc), cross linked data with other databases (UniProt and Pfam) and structural information of the protein (RMSD, oligomeric state, conformers, etc). It allows the exploration of conformational diversity and its determinants at the quaternary level, for a large number of proteins determined under different experimental conditions and from a wide variety of families and species.
Software & tools
SCPE
(Structurally Constrained Protein Evolutionary model)
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.
BeEP
(Best Evolutionary Pattern)
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.
If you use BeEP please cite:
Palopoli, N, Lanzarotti, E, Parisi, G. BeEP Server: using evolutionary information for quality assessment of protein structure models. Nucleic Acids Res. Jul;41(Web Server issue):W398-405. 2013. (ISSN 0305-1048).
PCDB
(Protein Conformational Database)
PCDB is not currently active. Please use CoDNaS instead.
PCDB was a database of protein conformational diversity. For each represented domain, the database contained the redundant compilation of all corresponding different crystallographic structures. These structures represented the solved structure of the same domain under different conditions and could be consequently considered as different instances of the protein native fold. As a measure of the conformational diversity we used 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 made 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 used PCDB please cite:
Juritz E, Fernandez Alberti S, Parisi G. PCDB: A database of protein conformational diversity. Nucleic Acids Res. 2011 Jan;39(Database issue):D475-9. doi: 10.1093/nar/gkq1181. (ISSN-L 0305-1048)