Paper Citing NAMD - Abstract
Fataftah, Hiba; Karain, Wael
Detecting protein atom correlations using correlation of probability of recurrence
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82:2180-2189, SEP 2014
The dynamic cross-correlation Map(DCCM) technique has been used extensively to study protein dynamics. In this work, we introduce the use of the method of correlation of probability of recurrence (CPR) as a complementary method to detect correlation correlations between protein residue atoms. Time series of the distances of the C-a atoms of the beta-lactamase inhibitory protein (BLIP) from a reference position are analyzed using CPR and mutual information (MI). The results are compared to those provided by DCCM. In comparison to MI, CPR is found to detect more of the correlations present in DCCM. It is also able to detect a small number of significant correlations between distant residues that are not detected by DCCM
