Codes and Resources
Gaussian-weighted RMSD superposition of proteins
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Many proteins contain flexible structures such as loops and hinged domains. A standard RMSD (sRMSD) alignment of two different conformations of the same protein can be skewed by the difference between the mobile regions. To overcome this problem, we have developed a novel method to overlay two protein conformations by their atomic coordinates using a Gaussian-weighted RMSD (wRMSD) fit. The algorithm is based on the Kabsch least-squares method and determines an optimal transformation between two molecules by calculating the minimal weighted deviation between the two coordinate sets.
Our second technique, a local wRMSD fit, uses subsets of the protein sequence for an initial, local sRMSD alignment and then performs a wRMSD fit of the entire protein, keeping the Gaussian scaling factor set to 2 Å² to maintain the local bias in the fit. The optimal solution is identified by the largest %wSUM. Using this second method, we were able to achieve multiple alignments based on different domains of the protein, and the solutions could be ranked by %wSUM.
Damm, K.L. and Carlson, H.A. Gaussian-Weighted RMSD Superposition of Proteins: A Structural Comparison for Flexible Proteins and Predicted Protein Structures. Biophys. J. 2006, 90, 4558-4573.