Protein Fold Recognition and Comparative Modelling using HOMSTRAD, JOY and FUGUE

This article illustrates how tools exploiting the knowledge of protein three-dimensional structure can be used to identify homologues of known structure, generate sequencestructure alignments and assist model building. The tools described here include HOMSTRAD, a database of structure-based alignments for protein families of known structure, JOY, a program to annotate local environments in structure-based alignments, and FUGUE, a program to perform sequence-structure homology recognition. After a brief review of the whole process of homology recognition and comparative modeling, a specific example clarifies all the steps involved. This type of analysis will help obtain a better understanding of the function of many proteins whose sequences are known.