Hello there!
I am trying to dock ZIF-8 (MOF) with the drug doxorubicin using PyRx and discovery studio for visualization of results. My queries are:
1. When I convert .cif file to .pdb using openbabel, then the whole structure of MOF is deleted except few bonds. But, when I use discovery studio for this purpose, then it slightly changes its structure. (any better suggestion?)
2. Since, ZIF-8 is considered as a macromolecule as compared to the drug (doxorubicin). When I load the molecule on PyRx, split models are generated. From there, I am confused how to convert them to .pdbqt format? If I convert them 1 by 1 to .pdbqt, then I won't be able to select all the .pdbqt at the time of docking.
Kindly help me through this!
Pictures are attached for reference. Thanks
Do you have any literature for this kind of "docking"? what is the binding site here?
Regarding the conversion: You can use avogadro, DS, Gaussview etc there are many softwares for this purpose:
see here:https://www.iucr.org/resources/cif/software
Chemdraw, chemsketch also usefull.
Yes, here is the link: https://pubs.rsc.org/en/content/articlelanding/2012/ra/c2ra21087h.
Thanks brother, got my work done with the help of vesta
One problem is that the pdb format is a very poor format choice for small molecule structural data. It is a very old format, dating back to times when computer memory was incredibly expensive, and bound to the limits of punched cards as input. The .pdb format was developed to store crystallographic results for biological macromolecule structures, which use few standard building blocks, e.g. amino acids and nucleotides over and over again. It stores only the atom coordinates, and relies on the processing program to contain an internal dictionary providing the chemical details for each type of building block (residue), e.g. bond orders, charges, forcefield parameters etc., depending on the needs and purpose of that program. Display programs use distance criteria to draw the bonds between the atoms and get the bond order details from their internal dictionary. Docking, energy minimization and molecular dynamic programs for macromolecular structures similarely rely on internal dictionaries, but may allow you to extend these dictionaries as needed for modified residues and small molecules.
In contrast, it is simply not feasible to formulate an exhaustive dictionary for all possible small molecules. Small molecule chemical data file formats like .mol2 or .sdf need to store all information about the molecule (https://docs.chemaxon.com/display/docs/formats_mdl-molfiles-rgfiles-sdfiles-rxnfiles-rdfiles-formats.md ). The .cif format (crystallographic interchange format) is mainly designed to hold information about the crystal structure (such as unit cell values, atom names and their coordinates and any structural model quality indicators, e.g., R Factor) as well as any details of the diffraction experiment (such as temperature, pressure, experimental wavelength and the type and name of equipment used) and any data processing undertaken (such as the programs used to process the data) ( https://www.ccdc.cam.ac.uk/community/access-deposit-structures/deposit-a-structure/guide-to-cifs/#what-in-a-cif ). The related xpdb/mmCIF format is used by the protein database as a successor of the .pdb format
A .pdbqt file contains, in addition to the information from the pdb file, information on the charges (partial and full) on the different atoms. If this information can not be generated from the input and/or residue dictionary, no valid pdbqt file can be generated.
Thank you Professor @Annemarie Honegger for such detailed answer. Since, I have used vesta to confine the geometry of the crystalline strucuture of the ZIF-8 and it actually worked. No bonds were disturbed and got the whole structure intact. I hope it is correct, also found some references related to this trial.
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