What is the best alghorithm to superpose two protein? Same in sequence vary in shape?

09 September 2018 1 10K Report

these two algorithms seems fast and efficient for aligning (superpose) two proteins:

Acta Chrystallogr. Sect. A 61 (2005) 478

[doi: 10.1107/S0108767305015266] J. Comput. Chem. 31 (2010) 1561

[doi: 10.1002/jcc.21439]

This is apparently a fast and efficient method to obtain the optimal rotation matrix. Being so new (particularly the second), I don't think VMD has this method implemented, and I wonder if it could benefit from it, especially when a great number of structures have to be aligned (as with the RMSDTT plugin).

Xiaohui Wang

The cpptraj, gromacs tools also implement RMSD and superposition algorithms. You may check them.

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