Hi Darrel, what a wonderful introduction! How do you make multiple mutations at the same time and find out which combination has the lowest energy? Or is it possible to check multiple mutations using this program?
Hey, I just had a question regarding how to determine the minimization steps used in chimera? What is a good representative no. of minimization steps that the protein might take to accommodate a point mutation. Is 15 ideally a good no. of minimization steps that we can be confident about? Meaning, generally a protein might accommodate 15 steps ?
This video is very useful to me, thank you very much for the creator of this video. I also want to know how to use this software to add residues to complete the structure.
Loop modeling is the most immediate technique that could be applied. There are tools in Chimera to do this, but they also require another software, MODELLER, which is freely available to academic researchers, but not to government or commercial entities without a fee. www.cgl.ucsf.edu/chimera/1.5.2/docs/ContributedSoftware/model/model.html
The simple answer is “no,” but it also depends on the nature of the mutation that was introduced. If the change is minor, like from alanine (A) to glycine (G) or perhaps serine (S) to cysteine (C), then minimization is probably not needed. But if the mutation introduces different chemistry or charged moieties, even though there might not be a steric clash, the new chemistry might induce changes that would benefit from minimization. An example might be leucine (L), aspartate (D), and asparagine (N). They all have the same overall shape, but their “through-space” interactions would be very different. Hope this helps!
it is amazing how watching 10 min of video can save you from reading 1000 pages long manual.
Great, really useful tutorial!
I knew it was proteins... good pictures!
both vids very good. do make more
Hi Darrel, what a wonderful introduction! How do you make multiple mutations at the same time and find out which combination has the lowest energy? Or is it possible to check multiple mutations using this program?
very infomative.
Thanks King
again thanks I'm was looking exactly this.... but what happen when is a new mutation how the rotamer works in that case?
Hey, I just had a question regarding how to determine the minimization steps used in chimera? What is a good representative no. of minimization steps that the protein might take to accommodate a point mutation. Is 15 ideally a good no. of minimization steps that we can be confident about? Meaning, generally a protein might accommodate 15 steps ?
Can we save the generated mutant and use it for the molecular docking purposes, i was trying to do docking on mutant proteins......
Hey the minimization isn't working for me, do you happen to have the PDB for your molecule?
This video is very useful to me, thank you very much for the creator of this video.
I also want to know how to use this software to add residues to complete the structure.
Loop modeling is the most immediate technique that could be applied. There are tools in Chimera to do this, but they also require another software, MODELLER, which is freely available to academic researchers, but not to government or commercial entities without a fee. www.cgl.ucsf.edu/chimera/1.5.2/docs/ContributedSoftware/model/model.html
It is really useful demo, thank you sir.
I'm having one doubt. is it necessary to do energy minimization, if no clash found?
The simple answer is “no,” but it also depends on the nature of the mutation that was introduced. If the change is minor, like from alanine (A) to glycine (G) or perhaps serine (S) to cysteine (C), then minimization is probably not needed. But if the mutation introduces different chemistry or charged moieties, even though there might not be a steric clash, the new chemistry might induce changes that would benefit from minimization. An example might be leucine (L), aspartate (D), and asparagine (N). They all have the same overall shape, but their “through-space” interactions would be very different. Hope this helps!
How is this worked.