CDHIT http://weizhongli-lab.org/cd-hit/

If you mean clustering multiple conformations of the same protein, then most molecular modeling/visualization software have such tools. See, for example, "gmx cluster" or clustering plugin for VMD.

thanks @Dmitri Kireev and @Abhishek Kumar, but I am not looking for a certain software but rather an approach that can be turned or implemented as a software. For example, is it right to use K-means algorithm or RSMD or both!

particularly, I am looking for a suggested computational approach for protein structures clustering!

If "clustering multiple conformations of the same protein" is what you need, then all-atom RMSD would be an appropriate metric of the likelihood, and k-means would be fine as a clustering technique.