Hi,
I am having problem using chimera for receptor-ligand docking. There are two issues.
1. If I have a protein can I generate a pdb file for its homolog (the sequence of which is known).
2. If I know a protein (pdb) and ligand (smiles), how can I select the docking space box and place it exactly where I want. Basically how can I know the coordinates of the receptor central channel.
Regards,
Pratik
You can generate a pdb file of the homologue from its sequence using the protein as a template.
You can place the grid box by moving it around, you can drag the box and resize it. Let the visual feedback guide you. You don't need the coordinates. There are video tutorials available (https://youtu.be/qr079hiTOFc?t=1m46s).
@Uttam: Thanks for the video link, It worked fine.
But, how can I use protein template to generate pdb file of a homologue. Any links for this too, please.
Dear Pratik Ramjivan
1. SWISS-MODEL, I-TASSER and MODELLER
2. use grid box
Best
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