Description Format Details See Also Examples
This sample structure data consists of the amino acids names forming tunnels and their numbers is analyzed protein. The data is a result of CAVER which is a software tool for analysis and visualization of tunnels and channels in protein structures.
A structure object with three elements:
A matrix of characters "S" and "N" marking on sequence the structural element; "S" - amino acid forms the analyzed structure, "N" - amino acid which does not form the structure. Number of rows of the matrix corresponds to the number of structures analyzed
A vector containing the numbers of the amino acids in the sequence of interest (no gaps)
A matrix of numeric values: probabilities of corresponding to the structural information from first element of the output, which helps to reduce the effect of non-consistent structural amino acids on the conservativity analysis of the structure of interest
The tunnel analysis with CAVER was performed on human epoxide hydrolase structure (PDB ID: 4JNC) 50ns MD simulation.
CAVER: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002708
4JNC: http://www.sciencedirect.com/science/article/pii/S0960894X13004885
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