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Homology Modeling The following document gives some indepth information about homology modeling. A basic version can be found here. A modeling tutorial using DS Modeling (Accelrys) can be found here. Due to the well-known fact that amino acid sequence homology at a given level leads to similar 3D structure of proteins, several databases are interrelating the databases of sequences and structures. However, the term homology, a fundamental concept in bioinformatics, is often used incorrectly . Sequences are homologous if they are related by divergence from a common ancestor (as a first consequence, the search for homology in the sequence database is used to determine indications for function of proteins). Conversely, analogy relates to the acquisition of common structural or functional features via convergent evolution from unrelated ancestors . Homology is not a measure of similarity, but rather an absolute statement that sequences have a divergent rather than a convergent relationship. Among homologous sequences we can distinguish orthologs (proteins having the same function in different species) and paralogs (proteins performing different but related functions within one organism). The model building of a target structure based on the comparison with the data extracted from homologous sequences with known structures (parents or templates) is named comparative modelling. Besides, this can be extended to homologs with low percentage of identity. All current comparative modelling methods consist of four sequential steps :1) fold assignment and template selection; 2) template-target alignment; 3) model building; and 4) model evaluation.
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