Enhanced functional annotation of protein sequences via the use of structural descriptors

In order to circumvent limitations of sequence based methods in the process of making functional predictions for proteins, we have developed a methodology that uses a sequence-to-structure-to-function paradigm. First, an approximate three-dimensional structure is predicted. Then, a three-dimensional descriptor of the functional site, termed a Fuzzy Functional Form, or FFF, is used to screen the structure for the presence of the functional site of interest (Fetrow et al., 1998; Fetrow and Skolnick, 1998). Previously, a disulfide oxidoreductase FFF was developed and applied to predicted structures obtained from a small structural database. Here, using a substantially larger structural database, we expand the analysis of the disulfide oxidoreductase FFF to the B. subtilis genome. To ascertain the performance of the FFF, its results are compared to those obtained using both the sequence alignment method BLAST and three local sequence motif databases: PRINTS, Prosite, and Blocks. The FFF method is then compared in detail to Blocks and it is shown that the FFF is more flexible and sensitive in finding a specific function in a set of unknown proteins. In addition, the estimated false positive rate of function prediction is significantly lower using the FFF structural motif, rather than the standard sequence motif methods. We also present a second FFF and describe a specific example of the results of its whole-genome application to D. melanogaster using a newer threading algorithm. Our results from all of these studies indicate that the addition of three-dimensional structural information adds significant value in the prediction of biochemical function of genomic sequences.