[gmx-users] PDB structure quality

Mark Abraham Mark.Abraham at anu.edu.au
Fri Apr 3 05:35:20 CEST 2009

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.


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