Disordered proteins disorder prediction

Linding, R., L. J. Jensen, F. Diella, P. Bork, T. J. Gibson, and R. B. Russell. 2003. Protein disorder prediction Implications for structural genomics. Structure 11 1453-9. 

In the field of bioinformatics, avaUability of disorder prediction algorithms has enabled proteome-scale analysis of disorder propensity and correlation of disorda- with function [17-24]. Ordered and disordered proteins have diffeent roles in cellular processes. Whereas ordered proteins tend to be... 

Deng, X., Eickholt, J., Cheng, J. (2012) A comprehensive overview of computationeil protein disorder prediction methods. Mol Biosyst, 8(1), 114-121. 

The accuracies of the various PONDRs were estimated (Table IV) by applying them to the ordered sequences in 0 PDBS25 as summarized in Table II and to the merged set of disordered proteins described in Table I. Overall, the prediction accuracy of each PONDR was much better on the 222,116 ordered residues of 0 PDBS25 than on the 18,833 residues of the merged disorder set. Thus, prediction of order generalized much better than prediction of disorder. 

VL-XT gave a false positive prediction of disorder of 20% on a per-residue basis (Table IV) this error decreases to 0.4% for consecutive predictions of 40 or longer (Romero etal., 2001). These error rates lead to 6% of the nonredundant proteins from PDB having consecutive false positive predictions of disorder >40 residues in length. As discussed in... 

Ward JJ, Sodhi JS, McGuffin LJ, Buxton BE and Jones DT (2004) Prediction and functional analysis of native disorder in proteins firom the three kingdoms of life / Mol Biol 337,635-645. 

On the basis of all this evidence, the possibility must be remote that Ci and cellobiohydrolase activities do not reside in the same protein. The separation of so many different components all with Ci/cellobiohydrolase activity must be good evidence that Ci can be identified with cellobiohydrolase. Clearly, there are good grounds for questioning the basic tenet of Reese s hypothesis, namely, that the function of Ci is to produce some disorder between the cellulose chains only the prediction that two components are required for hydrolysis of highly ordered cellulose is confirmed. 

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