MARA is here to aid in your cheminformatic workflows
We are thrilled to showcase the incredible capabilities of this powerful tool. In this example we will highlight a daily workflow for a cheminformatic scientists. These incredibly important scientists aim to understand how the physical properties of a molecule can inhibit or lead to a(n) (un)wanted chemical interaction. While there are many possible tasks for a cheminformatician, today we focus on creating a library of molecules by specifically varying the R-groups of .SDF file we obtain by querying the ligand of an RCSB PDB file. We will then create an .SDF file for each molecule, add hydrogens, and minimize to be used later for docking studies.
Here, we outline the potential MARA workflow for a cheminformatician, illustrating how MARA can revolutionize your research and elevate your work to new heights.
Overall Workflow
- Download a ligand from a PDB ID
- Show an atomistic colored 2D representation of the ligand
- Label each atom with the proper index
- Generate new molecules as SMILES containing various groups at position 5:
- methyl
- ethyl
- methoxyl
- Convert all new SMILES to .SDF files
- Show structures
For this example we will use the RCSB PDB as the source of our molecular structure and we will obtain the structure using natural language. Any common source of molecular structure (SMILES, XYZ, SDF) can be used instead. Position 5 refers to carbon atom #5 as defined in the atom indices from the labeled 2D image. Users can easily define the chemical R-groups they would like to incorporate into the study and the location at which they should be substituted. MARA can then perform the operation and export a list of SMILES as well as .SDF structure files.
Download and annotate a ligand SMILES formula from an RCSB PDB entry via natural language
MARA uses reasoning to perform requested tasks via natural language, when prompted “download ligand from pdb 5CEO and annotate the atom indices” MARA will skip downloading the full PDB file from 5CEO and instead download only the SMILES string, which is then used to pass through another tool to produce a 2D drawing of the molecule with all atoms labeled according to the ligand entry in 5CEO.
Modification of a molecular scaffold using common terms for R-groups
MARA understands the basic conversions of standard chemical compounds to SMILES. This makes using natural language to create a library of R-groups at a molecular scaffold incredibly easy and less time consuming. Completion of tasks on a batch level allows many SMILES strings to be converted to many molecular structures automatically.
Want to try MARA out yourself? Click here to start with some free credits.