A protein conformational search space defined by secondary structure contacts.
A conformational search space describing the relative position and orientation of protein secondary structure elements in three-dimensions was defined. These spatial relations were encoded by homogeneous transformation 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 secondary structure elements, which were approximated by standard (phi, psi) assignments, was sufficient to reproduce accurately the core structure of proteins with known three-dimensional structures.
Département d'Informatique et de Recherche Opérationnelle, Université de Montréal, Québec, Canada. parisien/major@iro.umontreal.ca
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Parisien
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Major
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Peitsch
D000595:Amino Acid Sequence; D001665:Binding Sites; D003196:Computer Graphics; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D016213:Cyclins / Q000737:chemistry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017433:Protein Structure, Secondary
D016213:Cyclins