FROST: a filter-based fold recognition method

To assess the reliability of fold assignments to protein sequences, we developed a fold recognition method called FROST (Fold Recognition-Oriented Search Tool) based on a series of filters and a database specifically designed as a benchmark for this new method under realistic conditions. This benchmark database consists of proteins for which there exists, at least, another protein with an extensively similar 3D structure in a database of representative 3D structures (i.e., more than 65% of the residues in both proteins can be structurally aligned). Because the testing of our method must be carried out under conditions similar to those of real fold recognition experiments, no protein pair with sequence similarity detectable using standard sequence comparison methods such as FASTA is included in the benchmark database. While using FROST, we achieved a coverage of 60% for a rate of error of 1%. To obtain a baseline for our method, we used PSI-BLAST and 3D-PSSM. Under the same conditions, for a 1% error rate, coverages for PSI-BLAST and 3D-PSSM were 33 and 56%, respectively.