PrDOS: prediction of disordered protein regions from amino acid sequence

Abstract

PrDOS is a server that predicts the disordered regions of a protein from its amino acid sequence (http://prdos.hgc.jp). The server accepts a single protein amino acid sequence, in either plain text or FASTA format. The prediction system is composed of two predictors: a predictor based on local amino acid sequence information and one based on template proteins. The server combines the results of the two predictors and returns a two-state prediction (order/disorder) and a disorder probability for each residue. The prediction results are sent by e-mail, and the server also provides a web-interface to check the results.

Figure 1.

An example of the prediction result page for HIV-1 NEF (PDB code: 2NEF). (A) The prediction result of the two-state prediction (disorder/order) is shown in this part. The red residues are predicted to be disordered at the given prediction false positive rate. (B) The plot of disorder probability of each residue along the sequence is shown in this part. Residues beyond the red threshold line in this plot are predicted to be disordered. The user can change the size of the plot through the web-interface.

Figure 2.

Diagram of sequence encoding scheme. The sequence information in a 27-residue window is converted into an input vector by aligning the elements in a certain order. For each site, the value of each element of PSSM for 20 amino acid types and the spacer information are appended to the input vector, thus total dimension of the input vector is 567 [=(20 + 1) × 27]