Protein structure and snps

Question

[H.Hasani]

Dear all,

I'm looking for a tool that predicts the protein's structure after inducing mutations (user input). Are you aware of such approach? A similar example is MutationMapper which gives the 3D structure if it is known.

Thanks

[Denise CS]

Can you give us an example of an altered protein with its 3D structure displayed in MutationMapper please?

[H.Hasani]

MutationMapper does not show the change, it shows only the region were the mutation is.

Answer 1

[fileyfood]

There is a tradeoff between speed and information for a mutation: (1) Fast, visual: tools like MutationMapperenter link description here and the G2P portal for visualizing location of mutations. (2) Stability predictors including FoldX, Rosetta, and ThermoMPNN: predict the impact of a mutation physically, taking up to a few seconds per mutation. (3) MDSimulation: Long running simulation of a protein, often taking minutes hours to model the dynamics for a protein with a mutation, performance heavily affected by size of the protein. Tools like GROMACS and VMD can be used for this.