Comparative Analysis Results

Profile Alignment Covariance Similarity
Your inputs:
2vl0_A.pdb , 3eam_A.pdb , 3rhw_A.pdb , 3tlu_A.pdb

ca_coordinates.zip :
PDB-formatted coordinates of C-alpha atoms used for construction of the elastic network models, for all the submitted structures.

The overlap of the conformational space for the structures, measured as the Normalized Bhattacharyya Coefficient (BC) and the Root Mean Squared Inner Product (RMSIP).

  • The BC is calculated for covariance matrices that represents approximately 70% of the proteins total normalized variance.
  • The RMSIP compares the overlap of the 10 lowest-frequency normal modes.

Both measure the similarity of the modes responsible for the largest deformations of each structure, but BC also takes into account the energetic separation between modes.

Each plot shows all pairwise comparisons for the aligned proteins, with comparisons of a protein to itself along the diagonal (these values are always 1). If the low-energy fluctuations of aligned C-alphas covers completely non-overlapping space, both measures will be 0. If they cover the exact same space the measures will be 1. Only the motions of C-alphas at positions without gaps across the entire alignment is expressed in the normal modes compared.

In the corresponding downloadable plot files (access by click "Download all results"), on the top and left side of the plot, a dendrogram shows the hierarchical clustering obtained from a complete linkage clustering with euclidian distances as implemented in the Python package clustermap.

BC score
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RMSIP score
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Reference

The BC is exp(-NDB2) where NDB is defined in Fuglebakk E, Echave J, Reuter N. Measuring and Comparing Structural Fluctuation Patterns in Large Protein Datasets. Bioinformatics 2012 28; 19:2431-2440 (Eq. 8).

The RMSIP is used in many studies, for example: Amadei A, Ceruso MA, Di Nola A. On the Convergence of the Conformational Coordinates Basis Set Obtained by the Essential Dynamics Analysis of Proteins' Molecular Dynamics Simulations. Proteins 1999 36:419-424