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Normal Mode Analysis: Protein movements and conformational changes modeling

Description: Normal mode analysis (NMA) investigates the slowest motions in macromolecular systems. NMA calculates vibrational normal modes that have the lowest frequencies, which describe the largest movements in a protein and are the ones that are functionally relevant in terms of bioactivity. These vibrational modes can be computed for the whole protein as well as for its active site. If you explore the total conformational changes of a protein you should compute modes for the whole protein. If you need to know which movements happen in the active site, you should calculate modes for the active site.

Requirements: The NMA requires 3D structures of a protein. In particular, such structures can be downloaded from the Protein Data Bank, as well as some other sources of 3D biological macromolecular structure data. The protein-ligand complex should be uploaded with the .pdb format (or any standard 3D format). In order to calculate modes for the whole protein it is very important that it has no missing amino acid inside of the residue sequence. If a protein does not meet this requirement, calculate modes only for the active site.

Output/Results:

You will receive a .pdb file with coordinates of the docked ligand and the table with the information as follows: This procedure provides several of the most vibrational modes and their animation.

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