For docking experiment , you can select protein structures having resolution above 2 angstrom. Avoid proteins structures solved at larger resolution. It is important because sidechain placements depends on the resolution. Better resolution means more accurate side chain placement.  Side chains play important role in ligand binding, they can cause steric hindrance, even wrong placement can form false cavity or pocket. So the preference is always high resolution structure .

Another consideration to have is whether you actually know the binding site or not.

If you know the binding site and just want to screen different molecules, or determine Kd, important residues, etc... you can have a look at the B-factors of the atoms that are in the vicinity of your molecules. Often, active site residues conformations are way more accurate than the other residues of the protein surface.

In that case, even at a low structure resolution, you can have reliable information.

Hi,

Resolution is a measure of the quality of the data that has been collected on the crystal containing the protein or nucleic acid. If all of the proteins in the crystal are aligned in an identical way, forming a very perfect crystal, then all of the proteins will scatter X-rays the same way, and the diffraction pattern will show the fine details of crystal. On the other hand, if the proteins in the crystal are all slightly different, due to local flexibility or motion, the diffraction pattern will not contain as much fine information. So resolution is a measure of the level of detail present in the diffraction pattern and the level of detail that will be seen when the electron density map is calculated. High-resolution structures, with resolution values of 1 Å or so, are highly ordered and it is easy to see every atom in the electron density map. Lower resolution structures, with resolution of 3 Å or higher, show only the basic contours of the protein chain, and the atomic structure must be inferred. Most crystallographic-defined structures of proteins fall in between these two extremes. As a general rule of thumb, we have more confidence in the location of atoms in structures with resolution values that are small, called "high-resolution structures".

Thanks everybody for clearing the doubt. As per as my protein is considered, the active site is known. But unable to get the B-factor in PDB. Or it needs to be calculated. Please help

The B-factors are given in the pdb bile (XXXX.pdb).

For each atom, there is its xyz coordinates, an occupancy factor (usually 1.0) and then the B-factor for the atom.

Hi Sayan,

I recommend visualizing the electron density map from the Uppsala, Sweden electron density server. Check the electron density  map (EDM) in your protein's region of interest, and see if the side chain placement is supported by the EDM. Often, in low resolution structures, crystallogrspher's will place side chains in reasonable conformations without side chain electron density. This information is reflected in B-Factors as well. Together, B-Factors and by-eye analysis of the EDM should give a better idea of the accuracy of the binding site's crystal structure than overall resolution alone.

http://eds.bmc.uu.se/eds/  

Cheers,

Trevor Zandi

Thanks for the answer

You should be very careful about the reported X-ray or NMR models. Databases such as PDB does not validate the structures. Here's a link to a very informative lecture by John Berrisford of PDBe regarding this issue:

https://www.ebi.ac.uk/training/sites/ebi.ac.uk.training/files/materials/2014/140407_EMBO/6_-_pdbe_validation_-_john_berrisford.pdf

Thanks for the reply

Which are the factors affect the molecular docking process?

Dear Uttam Pal,

I can't find the lecture of John Berrisford, could you please send me the pdf file.