I prefer to join 2 drug molecules (cocktail) using bioinformatics approach. Are there any tools available for it? Any software available where one can submit the individual structure of the drug molecules and receive the merged drug molecules?
Its an interesting thing...
Do check out this video for some help
https://www.youtube.com/watch?v=n5XpNlevt-U
I guess you can also use Chemsketch or Chemdraw to make hybrids..
Regards.
Dear Mr. Jobin Thomas, Thank You so much for answering my question. I just few clarifications.
1. Is the video link which you shared is for merging 2 ligand molecules alone? Or does it involve protein? Because I just want to merge 2 ligand molecules together.
2. Regarding Chemsketch or Chemdraw, as far as I know, we will be drawing the structure on our own. How will we know the attachments sites of ligands in such a way that we draw the apt merged ligand molecules?
Will be greatful if you could clear me.
Joining or merging two drug or ligand molecules together in bioinformatics is usually done using molecular modeling software, such as PyMOL, Chimera, VMD, etc. These software programs have various tools that allow you to combine two or more molecular structures into one.
There are also some online platforms that offer molecular modeling tools and services, including the integration of multiple drug or ligand molecules. Some examples include:
- Swiss-PdbViewer (DeepView)
- LigandScout
- LigPlot+
You can submit your drug/ligand structures to these platforms, and they will provide you with the merged structure. However, it's important to note that the accuracy and reliability of the results may depend on the quality of the input structures and the parameters used in the merging process. To ensure the best results, it's recommended to consult with an experienced bioinformatics researcher or to seek help from specialized service providers.
Dear Mr. Satyendra Singh,
Thank You so much for answering the query. I request you to clear my small doubt. In case of Swiss-PDBViewer, LigandScout and LigPlot+ is there provision to submit ligands online?
Swiss-PDBViewer, LigandScout, and LigPlot+ are standalone software programs that are not web-based and do not offer a provision for online submission of ligands. These programs need to be downloaded and installed on a local computer to use them. Once the software is installed, the user can load a protein structure file and a ligand file, and then perform various analyses using the software. However, some online protein structure analysis tools, such as the RCSB Ligand Explorer and Mol* Viewer, do offer a web-based interface that allows users to search for ligands online and visualize them in 3D within the context of a protein structure.
To join or merge two drug or ligand molecules together, you can utilize molecular modeling software that provides structure manipulation capabilities.
1. In PyMOL (https://pymol.org/pymol-command-ref.html), both commands provide different ways to merge or join molecules in PyMOL, so you can choose the one that best suits your specific needs.
The "bond" command is used to create a covalent bond between specific atoms or residues in two different molecules. The syntax for the "bond" command is as follows:
bond selection1, selection2
Replace "selection1" and "selection2" with the appropriate atom or residue selections in each molecule that you want to join.
The "fuse" command, on the other hand, is used to join two molecules together by merging their coordinates. This command creates a single, continuous molecule from the selected regions of the two molecules. The syntax for the "fuse" command is as follows:
fuse selection1, selection2
Replace "selection1" and "selection2" with the appropriate selections in each molecule that you want to fuse together.
2. SwissDock (http://www.swissdock.ch/): SwissDock is an online docking platform that allows you to interactively dock ligands and perform structure manipulations. While it focuses on docking, it also provides basic editing functions that may help you merge drug molecules.
3. MolView (https://molview.org/): MolView is an online platform for visualizing and editing molecular structures. It supports importing and manipulating structures, which you can use to merge drug molecules.
Susanta Roy Very many thanks for answering my query. I just have one more query. Is there any possibility to check for synergism between 2 ligands when docked with a protein? That is multiple ligand dockings? Any protocols
do you know for that?
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