Related Experiment Video
Updated: Oct 3, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
A protein conformational search space defined by secondary structure contacts
M Parisien1, F Major, M Peitsch
1Département d'Informatique et de Recherche Opérationnelle, Université de Montréal, Québec, Canada. parisien/major@iro.umontreal.ca
Abstract:
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.
Related Concept Videos
Protein Organization
Protein Folding
Protein Folding
Conserved Binding Sites
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Protein Organization
The primary structure of a protein is its amino acid sequence.
Protein Folding
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...

