To facilitate understanding of, and access to, the information available for protein structures, we have constructed the Structural Classification of Proteins (scop) database. This database provides a detailed and comprehensive description of the structural and evolutionary relationships of the proteins of known structure. It also provides for each entry links to co-ordinates, images of the str...

We present an automated procedure to assign CATH and SCOP classifications to proteins whose FSSP score is available. CATH classification is assigned down to the topology level and SCOP classification to the fold level. As the FSSP database is updated weekly, this method makes it possible to update also CATH and SCOP with the same frequency. Our predictions have a nearly perfect success rate whe...

In protein research, structural classifications of protein domains provided by databases such as SCOP play an important role. However, as such databases have to be curated and prepared carefully, they update only up to a few times per year, and in between newly entered PDB structures cannot be used in cases where a structural classification is required. The Automated Protein Structure Identific...

Protein tertiary structures are known to have significant correlations with their biological functions. To understand the information of the protein structures, Structural Classification of Protein (SCOP) Database, which is manually constructed by human experts, classifies similar protein folds in the same domain hierarchy. Even though this approach is believed to be more reliable than applying...

Hidden Markov Models (HMMs) are probably the most powerful tool for the detection of protein sequence homology [4]. Maximization of their capabilities and biological usefulness requires the correct interpretation of their scores, and sufficient coverage of the sequence variations that exist in different protein families. Using information available from the SCOP database we investigated optimal...

The ASTRAL compendium provides several databases and tools to aid in the analysis of protein structures, particularly through the use of their sequences. It is partially derived from the SCOP database of protein domains, and it includes sequences for each domain as well as other resources useful for studying these sequences and domain structures. Several major improvements have been made to the...

MOTIVATION Protein families can be defined based on structure or sequence similarity. We wanted to compare two protein family databases, one based on structural and one on sequence similarity, to investigate to what extent they overlap, the similarity in definition of corresponding families, and to create a list of large protein families with unknown structure as a resource for structural genom...