PredictProtein

PredictProtein (Rost et al., 1994) uses a slightly different approach in making its predictions. First, the protein sequence is used as a query against SWISS-PROT to find similar sequences. When similar sequences are found, an algorithm called MaxHom is used to generate a profile-based multiple sequence alignment (Sander and Schneider, 1991). MaxHom uses an iterative method to construct the alignment: After the first search of SWISS-PROT, all found sequences are aligned against the query sequence and a profile is calculated for the alignment. The profile is then used to search SWISS-PROT again to locate new, matching sequences. The multiple alignment generated by MaxHom is subsequently fed into a neural network for prediction by one of a suite of methods collectively known as PHD (Rost, 1996). PHDsec, the method in this suite used for secondary structure prediction, not only assigns each residue to a secondary structure type, it provides statistics indicating the confidence of the prediction at each position in the sequence. The method produces an average accuracy of better than 72%; the best-case residue predictions have an accuracy rate of over 90%. Sequences are submitted to PredictProtein either by sending an E-mail message or by using a Web front end. Several options are available for sequence submission; the query sequences can be submitted as single-letter amino acid code or by its SWISS-PROT identifier. In addition, a multiple sequence alignment in FASTAformat or as a PIR alignment can also be submitted for secondary structure prediction. The input message, sent to predictprotein@embl-heidelberg.de, takes the following form: After the name,affiliation, and address lines, the # sign signals to the server that a sequence in oneletter code follows. The sequence format is essentially FASTA, except that blanks are not allowed. For this alignment, the phrase do NOT align before the line starting with # assures that the alignment will not be realigned. Nothing is allowed to follow the sequence. The output sent as an E-mail message is quite copious but contains a large amount of pertinent information. The results can also be retrieved from an ftp site by adding a qualifier return no mail in any line before the line starting with #. This might be a useful feature for those E-mail services that have difficulty handling very large output files. The format for the output file can be plain text or HTML files with or without PHD graphics. The results of the MaxHom search are returned, complete with a multiple alignment that may be of use in further study, such as profile searches or phylogenetic studies. If the submitted sequence has a known homolog in PDB, the PDB identifiers are furnished. Information follows on the method itself and then the actual prediction will follow. In a recent release, the output can also be customized by specifying available options. Unlike nnpredict, PredictProtein returns a reliability index of prediction for each position ranging from 0 to 9, with 9 being the maximum confidence that a secondary structure assignment has been made correctly. The results returned by the server for this particular sequence, as compared with those obtained by other methods, are shown in modified form in Figure 11.4.