Gathers information on proteins. CASP is an online resource that assists users in identification of protein structure from sequence. It offers several methods to work on the protein topic and aims to establish state of the art in protein structure prediction. It also highlights progress that have been made and where gaps are still present.
A repository for evolutionary conservation analysis of the proteins of known structures in the Protein Data Bank (PDB). Sequence homologues of each of the PDB entries were collected and aligned using standard methods. The evolutionary conservation of each amino acid position in the alignment was calculated using the Rate4Site algorithm, implemented in the ConSurf web server. The algorithm takes into account the phylogenetic relations between the aligned proteins and the stochastic nature of the evolutionary process explicitly. Rate4Site assigns a conservation level for each position in the multiple sequence alignment using an empirical Bayesian inference. Visual inspection of the conservation patterns on the 3D structure often enables the identification of key residues that comprise the functionally important regions of the protein. The repository is updated with the latest PDB entries on a monthly basis and will be rebuilt annually.
Provides a public repository for annotation of proteins. CDD includes more than 56 000 records from all sources database dispatched into 5 600 multi-model superfamilies. The database incorporates biomolecular sequences accompanied by the location of evolutionarily conserved protein domain footprints and links to functional sites related to them. Searches can be made by protein or nucleotide query, accession, GI number, or with a sequence in FASTA format.
Gives access to a collection of conservation of residue positions in folds across protein families. CoC can be used to find key functional residues and/or structural residues to be studied through experiment. It is useful to retrieve amino acids that are important for protein function and folding. This tool contains over 3 000 proteins, which cover all known protein structures in the Protein Data Bank.