Related Experiment Video
Updated: Sep 17, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
ProSup: a refined tool for protein structure alignment
P Lackner1, W A Koppensteiner, M J Sippl
1Center for Applied Molecular Engineering, Institute for Chemistry and Biochemistry, University of Salzburg, Jakob-Haringer Str. 3, A-5020 Salzburg, Austria.
Abstract:
We investigated and optimized a method for structure comparison which is based on rigid body superimposition. The method maximizes the number of structurally equivalent residues while keeping the root mean square deviation constant. The resulting number of equivalent residues then provides an adequate similarity measure, which is easy to interpret. We demonstrate that the approach is able to detect remote structural similarity. We show that the number of equivalent residues is a suitable measure for ranking database searches and that the results are in good agreement with expert knowledge protein structure classification. Structure comparison frequently has multiple solutions. The approach that we use provides a range of alternative alignments rather a single solution. We discuss the nature of alternative solutions on several examples.
More Related Videos
Related Concept Videos
Protein and Protein Structure
Structural Protein Function
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity. In bones and teeth, it mineralizes to form...
Protein Folding Quality Check in the RER
Protein Organization
The primary structure of a protein is its amino acid sequence.
Structural Protein Function
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity. In bones and teeth, it mineralizes to form...
Protein and Protein Structures

