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I have an ensemble of homology models of a protein, and I now wish to remove those models which have backbone clashes. I could obviously check by eye but this is subjective and probably will not be accepted for publication.

What is the best (reproducible) method to determine if a particular protein model contains a backbone clash?

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up vote 3 down vote accepted

The way to check for steric clashing between any two atoms, backbone or otherwise, is to compute their Euclidean distance. If a and b represent two atoms (with a_x being the X coordinate of atom a and so forth), you can calculate their Euclidean distance as follows.

d(a, b) = sqrt( (a_x - b_x)^2 + (a_y - b_y)^2 + (a_z - b_z)^2) )

So essentially the idea would be to calculate the pairwise distance between each of the backbone atoms. For any pair of atoms, there is steric clashing if the distance between them falls below a certain threshold. If I remember correctly, this threshold is the sum of the van der Waals radii of the two atoms.

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I am assuming that the variables a and b represent atomic radii of the two respective atoms. So a_x is the atomic radii of a * the x co-ordinate? Wont this equation return an error if I try to square root a -ve number? To determine a steric clash I add the radii of atoms a and b and if this value is greater than the value from the equation I have a clash? –  harpalss Aug 22 '12 at 13:37
    
Yes, a and b are 3-dimensional vectors each containing the X, Y, and Z coordinates of the two atoms. However, the value inside the sqrt() will always be non-negative since each of the three differences is squared, so getting an undefined value shouldn't be a problem. I have updated the answer. –  Daniel Standage Aug 22 '12 at 13:56
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