Protein fold recognition

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PROTEIN FOLD RECOGNITION USING SEQUENCE PROFILES AND ITS APPLICATION IN STRUCTURAL GENOMICS... 

PROTEIN FOLD RECOGNITION USING SEQUENCE PROFILES... 

Fig. 3. The protein fold recognition protocol and fold prediction for complete genomes, (a) Construction of the FID library (b) fold prediction for proteins encoded in complete genomes. 

The 3D-PSSM (Kelley et ah, 2000) server at http //www.bmm.icnet.uk/ 3dpssm/ offers online protein fold recognition. On the submission form, enter your e-mail address and a one-line description of the query protein, then paste the query sequence into the sequence box and click the Submit button. The query sequence is used to search the Fold library for homologues. You will be informed of the URL where the result is located for 4 days. The output includes a summary table (hits with statistics models that can be viewed with RasMol classifications and links) and fold recognition by 3D-PSSM with a printout as exemplified in Figure 12.13. The alignment displays consensus sequence, secondary structures (C for coil, E for extended, and H for helix), and core score (0 for exterior to 9 for interior core). 

Figure 12.13. Protein fold recognition by 3D PSSB. The summary fold recognition results of cod alcohol dehydrogenase analyzed by 3D PSSB (secondary structure predic-...

PSIPRED Automatic sequence alignment, protein fold recognition, and secondary structure prediction web server 173 bioinf.cs.ucl.ac.uk/psipred/... 

The correctness of hits corresponding to families with known structural information is further verified by employing the protein fold recognition method PHYRE (Protein Homology/analogY Recognition Engine) version 0.2, which assesses the compatibility of a sequence to a three-dimensional structure (29). 

The commonly used benchmark for protein fold recognition is the test set suggested by Fischer et al. (1996), which comprises a set of 68 pairs of proteins with very low sequence similarity, but very highly similar folds. 

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