The DIRECT-ID method computes norm difference matrices from covariance matrices routinely computed after MD simulations. The norm surfaces can be used to (1) quantify the extent of difference in the dynamics and (2) extract structurally relevant features that contribute most prominently to the dynamics. These differences can be a function of solution conditions, ligand binding, etc.
Please cite the following article if you use DIRECT-ID in your research:
S.K. Lakkaraju, J.A. Lemkul, J. Huang, and A.D. MacKerell, Jr. (2016) "DIRECT-ID: An Automated Method to Identify and Quantify Conformational Variations - Application to β2-adrenergic GPCR." J. Comput Chem. 37: 416-425. DOI:10.1002/jcc.24231
HREX trajectories from the Klebsiella pneumoniae lipopolysaccharide study
Hamiltonian replica exchange input files and trajectories from the manuscript "Impact of branching on the conformational heterogeneity of the lipopolysaccharide from Klebsiella pneumoniae: Implications for vaccine design." See the README file in the .tgz package for a description of the contents.
Download description of input scripts and data files
Download input scripts and data files