In the PubChem database I could find a 2D structure of the compound (CID 24763) but wants a 3D structure for docking, moreover the compound is too long so is there any technique to cut it short since the compound is starch like polysaccharide??
Download the 2D and convert into 3D using Marvin sketch or chemsketch or chemdraw.
You can use OpenBabel https://open-babel.readthedocs.io/en/latest/3DStructureGen/Overview.html to convert the structures to 3D
You can open the already downloaded 2D file (sdf format) in CHEMDRAW. Thereafter, under Edit menu, click on ''Get 3D Model'' to display the 3D structure. To minimize the energy of the molecule before saving, Double-click on the centre of the displayed 3D structure to open it in a separate window or interface; and then click on ''mm2'' (molecular mechanics 2) for the energy minimization. Lastly, save the molecule (3D structure) as a pdb file.
Anuraj Nayarisseri Sir, Thank you for the resource, which helped me to eradicate the problem.
- Badges
- Science topic
- Similar topics
- Biological Science
- Biochemistry
- Enzymology
- Enzymes