Some people already asked this question but I still can't understand what the rmsd values of Vina (ub and lb) means. So, my doubts are:
1) Why my first binding mode always gets 0 rmsd? Is it the best binding mode described on Vina's manual?
2) Whats the relevance of these rmsd values in my analyse? In fact, I ignored them in my last docking and the results were just fine.
To state it briefly. The first results is compared to itself, hence it will always be 0. Subsequent results are then compared to the first. A very small deviation indicates very minor changes in the conformation of the ligand, but usually describes an almost identical pose. It gets interesting when poses have substantial deviation in rmsd, but still exhibit comparably good docking scores. Those one should analyze carefully to conclude which pose reflects real binding. Sometimes that is not easy at all. If you have any experimental data to compare to, even the most basic SAR, that might be sufficient to discriminate the poses.
I agree with Peter Teriete. In fact when a molecule is subjected to dock at receptor's cavity. According to geometrical and physical nature of selected cavity, user defined numbers of the most complimentary and highest binding affinity having conformations of the ligand are generated. After that they were aligned to compare their displacement and conformational changes and result are reported in root mean square deviation (RMSD). The highest binding affinity having conformation will compare it self, so it will be always zero (0) Angstrom . The 2nd the highest binding affinity having conformation will compare to the highest, subsequently all.
Peter Teriete May I know what do mean by real binding please? are you mentioning the hydrogen bonds or the binding score?
Arthi Sivashanmugam , real binding is not a quantifiably term, I used it to refer to binding poses/modes that would occur under experimental conditions. Just because you get an acceptable docking score, that does not necessarily mean that a given pose occurs as such. As so often, the prove is in the pudding, meaning ideally you evaluate compounds and some close analogues under experimental conditions (some type of binding assay) to inform your docking model. This is of course not always possible, and I use docking models frequently to generate some new ideas for analogues and 'test-drive' them, but always with some big caveats in my mind.
Peter Teriete Thank you for the clear explanation. I missed the point in your first answer. Thank you :)
What is the meaning of lower bound and upper bound? How to calculate the absolute RMSD from these two values of RMSD given by Autodock Vina?
RMSD
RMSD values are calculated relative to the best mode and use only movable heavy atoms. Two variants of RMSD metrics are provided, rmsd/lb (RMSD lower bound) and rmsd/ub (RMSD upper bound), differing in how the atoms are matched in the distance calculation:
- rmsd/ub matches each atom in one conformation with itself in the other conformation, ignoring any symmetry
- rmsd' matches each atom in one conformation with the closest atom of the same element type in the other conformation (rmsd' can not be used directly, because it is not symmetric)
- rmsd/lb is defined as follows: rmsd/lb(c1, c2) = max(rmsd'(c1, c2), rmsd'(c2, c1))
Please see the reference: https://vina.scripps.edu/manual/
Hello, can anyone help to explain the lower bound and upper bound in detail?
Thanks a lot
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