Sequence alignment for molecular replacement

This article focuses on the key step of obtaining the best possible sequence alignment of the Query ( the protein you are interested in) to the Target ( a protein of known three-dimensional structure) in order to build a molecular model for molecular replacement. Common sequence-alignment methods are discussed, starting from structural alignment and then moving to pairwise, multiple and profile-profile methods. The limitations of sequence-alignment methods and guidelines on how to judge the likely accuracy of alignment are considered. This is not a detailed tutorial on how to use specific programs; rather, the reader is directed to current tools and techniques that are likely to yield good results.