Before revision:  Although many protein comparison methods are available online on numerous web servers, their ability to handle a large scale model comparison is often very limited. Most of the servers offer only a single pairwise structural comparison , and they usually do not provide a model-specific comparison with a fixed alignment between the models .
After revision:  Although many protein comparison methods are available online on numerous web servers, their ability to handle a large scale model comparison : (1) they operate with methods designed to compare actual proteins, not the models of the same protein, (2) majority of them offer only a single pairwise structural comparison , and they usually do not provide a model-specific comparison with a fixed alignment between the models .