Background: The hierarchical and partially redundant nature of protein structures justifies the definition of frequently occurring conformations of short fragments as `states'...
The 3D conformation of a protein may be compactly represented in a symmetrical, square, boolean matrix of pairwise, inter-residue contacts, or "contact map". The contact...
Jingjing Hu, Xiaolan Shen, Yu Shao, Chris Bystroff...
We describe and demonstrate the effectiveness of a method of predicting protein secondary structures, sheet regions in particular, using a class of stochastic tree grammars as rep...
Background: Accessible surface area (ASA) or solvent accessibility of amino acids in a protein has important implications. Knowledge of surface residues helps in locating potentia...
Shandar Ahmad, M. Michael Gromiha, Hamed Fawareh, ...
Background: Many structural properties such as solvent accessibility, dihedral angles and helix-helix contacts can be assigned to each residue in a membrane protein. Independent s...