Hi ,

High resolution crystal structures are not required to do energy minimization. it would be helpful to some extent for NMR structures.

i believe, it is necessary since the positions of the hydrogens are fixed manually during the crystal solving process, so it would be essential to go for energy minimization. But many people will not do this, but good journals demand this step.

No need. if you catch PDB from crystal or NMR

Thank you all for your valuable answers.

Http://macosxpostdoc.blogspot.tw/2011/05/brief-primer-in-energy-minimization-or.html

check the above link once , hope it would be helpful !

If you delete the bound ligand and optimize the pure protein, the binding cavity may disappear. Then you will have to force the new ligand somewhere in the protein, which will distort the protein, and this distortion is fairly ambiguous. Furthermore, it is implicit in your approach that the new ligand binds into the same cavity as the original, although it is also not proven.

A possibility for reducing the uncertainty would be to perform MD after a short minimization. The problem with it that the protein structure could change a lot, and you have to correctly characterize the environment: for transmembrane proteins by the bilayer all around, the solvation at the top and the bottom, counterions, reliable charges, etc. A good solution of the structural problem is far from a simple modification of the experimental structure.

For an enzyme, if it is embedded in aqueous solution, the X-ray structure can only be a starting point, explicit water is needed all around, counterions, and a long MD before you may believe that a reliable structure is being studied. As I wrote, some structural parts basically change. I ran an MD for a protein structure with a big hole in the experimental structure applying the implicit solvent approach, and the hole disappeared. It could stem in the solid phase from the interactions of the neighbors, crystal packing, or was filled with water, not appearing in the published PDB file. So the problem is manifold.

Typically you do want to do some minimization to optimize the positions of hydrogens which are added to crystal structures. For that you usually freeze or constrain all of the heavy atoms and only minimize the hydrogens.

@david reichert. as we know that proteins are not rigid hence if we minimise only hydrogen by teethering heavy atoms are we not forcing the lignad to use cavity appropriate for original ligand and in that process is there a chance to miss novel interactions.

Also as some proteins can have more than one cavity what if i want to dock in a different cavity. as protein is crystallized according to a certain ligand therefore can that effect other cavities as well ?

Minimising a protein is making the assumption that the forcefield better describes the geometry than the the crystal structure does. In truth it is simply not possible to answer this question. Minimising will often introduce bad geometry into a protein, particularly in cases where the forcefield being used is significantly different from that used to optimise the PDB from the x-ray difraction data. Sometimes minimisation will eliminate crystal-packing artifacts.

Essentially this question is no different from that of an experimentalist. Run the docking simulations using known ligands and see which procedure gives you better results. ALL docking experiments should be checked for suitability in any case. As a minimum you need to optimise the directions that the hydrogen are facing using a protonate protocol and then be able to reproduce the crystal structure if it has a bound ligand. Generally, programs are pretty good at reproducing a bound form (RMSD

The question is yes and no simulteanously. As Jason pointed out, the force field is not gonna describe better the protein bniding site than the reality observed in X-ray. However, the "YES" answeer comes when you analize the electron density map and you observe the position of some atoms or amino-acid moieties doesn't correspond to any density. In such cases, it would be worthy to minimize such atoms in order to achieve a better amino-acid orientation, but if the density is perfectly fitted to the protein coordinates, then, nothing special should be done, and therefore, no minimization should be carried out.

There is no definitive answer to your question, as it is case dependent. One thing you might want to check is the packing interactions within your protein crystal. Remember a crystal structure is a "solid state" structure (or rather semi-solid, because of the high water content in the protein crystals), so regions of the protein that look quite far from each other in the "monomer" protein might actually be very close from each other in the packed crystal, and their conformation might therefore be affected. It can be good to see if this happens in regions around your binding site.

I would definitely not minimize a structure without the ligand in, as the binding site might just collapse. I wouldn't minimize a structure all at once either. If you have the possibility of fixing/releasing specific atoms/residues, then:

1) Optimize hydrogen positions while keeping the rest fixed.

2) Release the side chains with high B factors, as they might be the one with the worst coordinates.

3) Release the other side chains.

4) Backbone is always the last to be released.

Check that your forcefield is appropriate for your simulation conditions. Some work better with explicit solvent, some not. Check the protonation state of your residues and ligands. Last thing: If you can, start minimization with a steepest descent algorithm, not with MD-based protocols that could send your atoms miles away if you have but a small bump in your starting structure.

Hope this helps.

@Jesus Seco Moral  could you please suggest a suitable software for electron density map visualization of cryatal structure? I can obtain it for minimized structure by loading mdcrd files. I dont know how to do it for the crystal structures. Isnt it imossible to obtain electron related data without any quantum calculation?

See, protein minimisation and protein preparation are two different protocols but both jobs are usually plugged in simultaneously in most programs. So, it is undoubtedly necessary to go for protein preparation if the resolution is not very high. However, you can skip the minimisation protocol.

Nevertheless, i would suggest you to go for both the protocols and judge yourself the accuracy of method by redocking the cocrystalised ligand prior to actual dock.

for most instances, i believe minimisation would make the force field efficient during the structural processing.