Hello everyone,
I work with amino-acid networks. Basically, I want to compare a network of a wild-type protein to the network of the same protein mutated in one position. The thing is, I want to do this for every (single) mutation possible. Therefore, if the sequence of my protein is of length N, I first need to produce the N*19 mutated proteins first. The network is defined by atomic distances so I need a structure for every mutation and I'm doing it in Silico. I know FoldX is not time consuming, both in terms of time it takes to produce the mutations and in terms of telling it what mutations I want (I only need a list of mutations).
I would like to know if there are other software than can do the same think as FoldX, that are time acceptable to produce many mutations, in my case 1577 mutations.
Thank you
When you mutate a residue, there could be steric clashes or other interactions. For this purpose you need to minimize the structure at least - MODELLER is a good choice for that. MD simulation would be ideal but very slow. MD can be done for few selected mutations using gromacs or other MD programs.
I think you're looking for massively parallelized molecular dynamics runs. Needs a TON of computational resources, and it's not gonna get done in an "acceptable" time frame, I can tell you that much.