Pfam is a collection of multiple sequence alignments and profile hidden Markov models (HMMs). Each Pfam HMM represents a protein family or domain. By searching a protein sequence against the Pfam library of HMMs, you can determine which domains it carries i.e. its domain architecture. Pfam can also be used to analyse proteomes […]
BLAST compares a sequence of DNA or amino acids to a massive database and returns information about how similar the sequences are.
The comparison of nucleotide or protein sequences from the same or different organisms is a very powerful tool in molecular biology. By finding similarities between sequences, scientists can infer the function […]
SCOP is a hierarchical classification of proteins. Top in the classification are large fold types and digging down leads to small group of similar proteins.
The site’s classification also produces some interesting statistics on the fold types of proteins which can be found on the site.
CATH is a protein structure classification database. The database is organized by Class, Architecture, Topology, and Homologous super-family.
For any given structure classified in the database, CATH gives you information on the structure and function of that protein. The evolutionary relationships involving the structure of interest and other proteins in the database can also […]
The Protein Data Bank (PDB) operated by the Research Collaboratory for Structural Bioinformatics (RCSB) is a premier catalog of large crystal models and NMR models of proteins. The database also includes methods for searching by nucleic acids and ligands.