Fold Recognition and Threading

Firth, J. Li, C. W. Murray. Protein fold recognition by threading comparison of algorithms and analysis of results. Prot. Eng. 1995, 8, 1197-1204. 

Inverse Folding and Threading (350-353). This is the ultimate in motif recognition One makes use of the ever-increasing database of known three-dimensional structures to generate a set of 3D folding motifs for proteins. The sequence of an unknown structure... 

R. T. Miller, D. T. Jones, J. M. Thornton. Protein fold recognition by sequence threading tools and assessment techniques. FASEB J. 1996, 10, 171-178. 

Several variants using multiple sequence information and sequence profiles generated for the query sequence for the threading process have been described and demonstrate to improve fold recognition performance [109, 195-203] similarly as has been observed for secondary structure prediction and sequence methods. 

Structure prediction methods have to be validated using comprehensive and representative benchmark sets. A couple of benchmark sets have been proposed [188, 199, 270] consisting of a fold library and a list of structurally similar protein pairs without significant sequence similarity. Such a benchmark [335] involves using the method in question to thread one protein of each pair against the library and to count the number of successful recognitions of the structural match or the number of correct identifications of related protein pairs. A couple of methods have been evaluated this way. 

For the CASP2 experiment, Marchler-Bauer and Bryant defined a large number of quantitative criteria [110] to be used by the assessor to judge and rank the models and prediction teams. These criteria include several measures for fold recognition specificity, for threading alignment specificity, threading contact specificity, and model accuracy. 

Panchenko, A. R., A. Marchler-Bauer, and S. H. Bryant, Combination of threading potentials and sequence profiles improves fold recognition. J Mol Biol, 2000. 296(5) p. 1319-31. 

Rost, B., R. Schneider, and C. Sander, Protein fold recognition by prediction-based threading. J Mol Biol, 1997. 270(3) p. 471-80. 

Several methods have been developed for this purpose. These include (a) comparative or homology modeling, (b) threading method or fold recognition, (c) ab initio method, and (d) visualization of protein folding by computer simulation. 

Fold recognition Protein structure can be predicted with fold recognition. A protein sequence and its predicted secondary structure are compared to the sequences of a library of experimentally known folds. If a structure has more than 50% sequence homology, homology modeling is used instead. A similar procedure is threading. 

Fold recognition by determining which regions of a query protein of known sequence (but unknown structure) share a folding pattern of protein structure(s) in the library. Two approaches, structure superposition (overlap) and threading are generally employed. The results, if found, are a nomination of a known structure that has the same fold as the query protein. 

---