Sep 01, 2020
Version 2
Building a molecule for docking using PubChem and YASARA V.2
This protocol is a draft, published without a DOI.
- 1James Madison University
Protocol Citation: Chris Berndsen 2020. Building a molecule for docking using PubChem and YASARA. protocols.io https://protocols.io/view/building-a-molecule-for-docking-using-pubchem-and-bekejcteVersion created by Chris Berndsen
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: April 03, 2020
Last Modified: September 01, 2020
Protocol Integer ID: 35174
Abstract
The database Pubchem is a good resource for finding the structure of small, organic molecules as well as information on the structure, function, and effects of these small molecules. This information can be useful for finding information on how a drug might function or the structure of the drug itself. Using the SMILES information from a PubChem, it is possible to extract the structure for building the small molecule in the modeling program YASARA. This 3-D structure is then the ligand for docking studies with a target protein or for other computational analyses.
Materials
internet connection
YASARAview
Find the structure of your molecule
Find the structure of your molecule
Navigate to PubChem
Search for the molecule name
Note
The molecule will like not be a protein, but a small molecule like glucose or maltodextrin. Searching for proteins is not useful.
Select an entry from the results and check to make sure that the molecule matches expectations.
Record the PubChem CID (found in the Title/Summary section at top) as a note in this step.
In section 3.1.4, copy the canonical SMILES code. Record it as a note on this step
Building the molecule in YASARA
Building the molecule in YASARA
Open YASARA
Go to Edit>Build>Molecule from SMILES string
Paste the SMILES string in the box and press OK
The resulting molecule will be built, however it may contain unusual geometry.
Right click on SMILES in the Scene Content table and select Name to rename the molecule. Record the name as a note on this step.
Save the molecule as a .PDB file. File>Save As>PDB file. Then save the file and upload to OSF
Name the file as
ligandname_smiles.pdb
Record the file location as a note on this step.