Modeller: Generation and Refinement of Homology-Based Protein Structure Models

Functional characterization of a protein sequence is one of the most frequent problems in biology. This task is usually facilitated by accurate three-dimensional (3D) structure of the studied protein. In the absence of an experimentally determined structure, comparative or homology modeling can sometimes provide a useful 3D model for a protein (target) that is related to at least one known protein structure (template). A 3D structure of proteins from the same family is more conserved than their primary sequences. Therefore, if similarity between two proteins is detectable at the sequence level, structural similarity can usually be assumed. Comparative modeling usually starts by searching the Protein Data Bank (PDB) of known protein structures using the target sequence as the query. This search is generally done by comparing the target sequence with the sequence of each of the structures in the database. Comparative modeling consists of five steps: (1) search for related protein structures, (2) selection of one or more templates, (3) target–template alignment, (4) model building, and (5) model evaluation. If the model is not satisfactory, some or all of the steps can be repeated. There are several computer programs and Web servers that automate the comparative modeling process. The first Web server for automated comparative modeling was the Swiss-Model server, followed by CPHModels and ModWeb. These servers accept a sequence from a user and return an all-atom comparative model when possible.