Chih-Ying Lin wrote:
HI
The program WHATIF can perform a proper validation of the structure.
But, it is not free software.
Can anyone tell me how to test the protein structure manually or by Gromacs?
What is the criteria to determine the quality of the structure?
That depends on your objective - but you have to define that. Ultimately
some protein structure generated by a piece of software has to match in
a relevant way the structure found in biological systems. What that
means varies with what experimental information you have available.
Various computational tools might assist in estimating that match.
Mark
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