A protein conformational search space defined by secondary structure contacts

摘要

A conformational search space descring the relative position and oreitnation of protein secondary structure elements in three-dimensions was defined. These spatial relations were encoded by homogeneous transfomration matrices between pairs of residues "in contact" in two different secondary structure elements. A database of all occurrences of spatial relations for five hydrophobic residues was built. The use of one residue contact per pair of secondayr structure elements, which were approxiamted by standard (PHI, psi) assignments, was sufficient to reproduce accurately the core structure of proteins with known three-dimensional structures.