Hi everyone,
Are there any other alternatives other than the MODELLER program that I can use to complete the missing residues in the crystal structures before running the simulations?
We can discuss your suggestions, thanks.
Because the programme I use completes the missing residues, especially the residues in the N-terminal and C-terminal regions of GPCRs as long-chain structures, and it doesn't seem easy to reach the real structure.
Hey there Ekrem Yaşar! So, about completing those missing residues in crystal structures, it's a bit of a puzzle, isn't it? Now, with all my flair, has a couple of suggestions that might tickle your scientific fancy.
1. **SWISS-MODEL:** It's another modeling program that you Ekrem Yaşar might want to take for a spin. Similar to MODELLER, it helps predict the structure of your protein based on known structures. Sometimes a fresh perspective can uncover new angles, you Ekrem Yaşar know?
2. **Rosetta:** This one is like the James Bond of protein structure prediction. It's versatile, powerful, and has a range of tools for refining structures. It might give you Ekrem Yaşar that extra edge you're looking for.
3. **I-TASSER:** A bit of an underdog, but don't underestimate it. I-TASSER is quite robust and often surprises researchers with its accuracy.
4. **Phyre2:** It's an easy-to-use online tool that might not have the complexity of some others, but it's quick and can be surprisingly effective.
Now, mind you Ekrem Yaşar, each tool has its strengths and weaknesses. What works best might depend on the specific quirks of your protein. Don't hesitate to try a couple and see which one dances best with your data.
And remember, in the wild world of molecular modeling, there's no one-size-fits-all solution. So, experiment, iterate, and maybe you'll uncover the missing pieces to your crystal structure puzzle.
Now, what are your thoughts on these suggestions, my research companion Ekrem Yaşar?
Besides the software recommended above, I think you can use charmm GUI directly to repair the missing residues, cause you need run the simulation next.
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