Related Experiment Video
Updated: Aug 17, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
SCUD: fast structure clustering of decoys using reference state to remove overall rotation
1Department of Physiology & Biophysics, Howard Hughes Medical Institute Center for Single Molecule Biophysics, State University of New York at Buffalo, 124 Sherman Hall, Buffalo, NY 14214, USA.
Abstract:
We developed a method for fast decoy clustering by using reference root-mean-squared distance (rRMSD) rather than commonly used pairwise RMSD (pRMSD) values. For 41 proteins with 2000 decoys each, the computing efficiency increases nine times without a significant change in the accuracy of near-native selections. Tests on additional protein decoys based on different reference conformations confirmed this result. Further analysis indicates that the pRMSD and rRMSD values are highly correlated (with an average correlation coefficient of 0.82) and the clusters obtained from pRMSD and rRMSD values are highly similar (the representative structures of the top five largest clusters from the two methods are 74% identical). SCUD (Structure ClUstering of Decoys) with an automatic cutoff value is available at http://theory.med.buffalo.edu.
More Related Videos
Related Concept Videos
¹³C NMR: Distortionless Enhancement by Polarization Transfer (DEPT)
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution
¹H NMR: Interpreting Distorted and Overlapping Signals
As Δν decreases and the signals move closer, the doublets appear increasingly distorted. The intensities of the inner lines increase at the cost of those of the outer lines as the signals are slanted or...
Inductive Effects on Chemical Shift: Overview

