A nice feature for CE-Symm would be to identify the number, type and length of secondary structure elements (SSE) of the repeats (or subunits) of a symmetric structure. This feature would have many applications, such as:
Discard those symmetries that contain less than a specified number of SSE: the false positives (FP) of symmetry where only one big helix per subunit is aligned could be identified and reported as C1.
Classify or cluster the domains, chains or proteins with their symmetry: classification options from general to specific could include: type of symmetry, number of repeats, type of SSE of the repeats (all-alpha, alpha-beta-alpha, etc) and finally cluster by alignment significance of repeats. A step towards automatic classification of the domains.
Provide statistics about the prevalence of the different types of SSE in the structure fold space.
From the current CE-Symm version the start and end residues of each repeat (or subunit) can be obtained, so with the data about the start and end residues for each SSE present in the domain or protein it is possible to calculate all of the properties of SSE in the individual repeats.
lafita
commented
8 years ago
A nice feature for CE-Symm would be to identify the number, type and length of secondary structure elements (SSE) of the repeats (or subunits) of a symmetric structure. This feature would have many applications, such as:
From the current CE-Symm version the start and end residues of each repeat (or subunit) can be obtained, so with the data about the start and end residues for each SSE present in the domain or protein it is possible to calculate all of the properties of SSE in the individual repeats.