ENCoM

 

ENCoM is a coarse-grained normal mode analysis method that is unique in the sense that the elastic constants the define the modes of movements are modulated by a potential force field and the surface area in contact between atoms belonging to different residues in the protein or nucleotides in RNA. The method has been applied to a number of questions, primarily thus far to proteins. We have used ENCoM to predict the effect of mutations on stability and applied it as a tool in protein engineering. We also use it to generate conformational ensembles that may be useful for a number of applications, including in the representation of ensembles for virtual screening. We are currently applying ENCoM to study allostery as well as signal transduction in GPCRs.


Whereas we have developed a very easy to use and convenient web-service to predict the effect of mutations and generate conformational ensembles, this is currently temporarily unavailable. All the results that could be obtained through the web interface can also be obtained via the stand-alone version of ENCoM that can be downloaded here or from Github (includes the necessary scripts). In order to facilitate its use, we have created a step-by-step tutorial. If you use ENCoM, please cite the original article31 as well as the tutorial article42, for which you will need the scripts here.