Protein structure threading techniques

Threading techniques try to match a target sequence on a library of known 3D structures by threading the target sequence over the known coordinates. In this manner, threading tries to predict the 3D structure starting from a given protein sequence. It is sometimes successful when comparisons based on sequences or sequence profiles alone fail due to a too low sequence similarity. 

Scientists carry out searches on databases. Each EST of interest can be compared with sequences in proteins, and the degree of match can be determined. A technique called threading is used. This involves using data on three-dimensional (3D) protein structure, coupled with knowledge of the physicochemical properties of amino acids, to determine if the amino acid sequence is likely to fold in the same way as a sequence for which the structure is known. In this way, more information about the putative target protein can be assessed. 

Lemer, C. M., Rooman, M. J., and Wodak, S. J. (1995). Protein structure prediction by threading methods Evaluation of current techniques. Proteins 23, 337-355. 

The contributions to this volume demonstrate that structural studies of fibrous /1-proteins, as well as prion and amyloid fibrils, have advanced rapidly thanks in large part to improved experimental techniques and better theoretical analysis of the ever-increasing structural data. It is also possible to learn from studies of naturally occurring silks (Dicko et al., this volume) howvariations in the conditions of production of silk threads from the same protein can produce a variety of /1-structures with very distinct... 

More distantly related structures can be modeled by the use of the process of threading. This is a computational technique by which the sequence of the protein of an unknown structure is threaded through a nom-edun-dant library of well-determined structures to determine which are compatible with the sequence. Basic statistical methods for predicting secondary structure, a helix and p sheet, have 80% veracity. 

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