Related Experiment Video
Updated: Sep 27, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
Protein fragment clustering and canonical local shapes
Cornelius G Hunter1, Shankar Subramaniam
1Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Illinois, USA.
Abstract:
A novel clustering method is used to cluster protein fragments by shape. The centroids (mean fragments from each cluster) form a basis set of structural motifs. A database of 156,643 seven-residue fragments is used, and eight different basis sets with varying levels of resolution are generated. Coarse basis sets contain tens of centroids and provide meaningful local shapes, which are more detailed than the traditional secondary structure categories. High-resolution basis sets contain thousands of centroids and can be used to model tertiary structure of longer segments. The basis sets generated fit nontraining set proteins with the expected accuracy.
Related Concept Videos
Protein Folding
Mass Spectrometry: Molecular Fragmentation Overview
One type of fragmentation pattern is the cleavage of a single bond in the molecular ion. The cleavage leads to a radical and a cation. The cleavage can occur at...
Protein Organization
The primary structure of a protein is its amino acid sequence.
Protein Organization
Protein and Protein Structure
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...

