Jpred

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The prediction of the secondary structures can be made by the structure similarity search of PDB collection at the site. Several servers provide such prediction method. The Jpred, which aligns the query sequence against PDB library, can be accessed at http //jura.ebi.ac.uk 8888/index.html. To predict the secondary structures, however, check Bypass the current Brookhaven Protein Database box and then click Run Secondary Structure Prediction on the home page of Jped to open the query page (Figure 12.10). Upload the sequence file via browser or paste the query sequence into the sequence box. Enter your e-mail address (optional) and click the Run Secondary Structure Prediction button. The results with the consensus structures are returned either online (linked file) or via e-mail (if e-mail address is entered). 

Figure 12.10. Query page of Jpred. Jpred aligns the input single sequence or unaligned multiple sequences to generate PSIBLAST profile and uses the profile for Jnetto produce prediction. Alternatively, the aligned multiple sequences can be supplied for Jnet prediction.

JPRED Secondary structure prediction and sequence alignment web server 170 www.compbio.dundee.ac.uk/ www-jpred/... 

Cuff JA, Clamp ME, Siddiqui AS, et al. JPred a consensus secondary structure prediction server. Bioinformatics 1998 14 892-893. 

JPRED [159, 160], or CODE [161] by systematically optimizing the performance on a training set by using decision-tree methods or machine-learning approaches such as support-vector machines [162]. 

JPRED [66,67] is a neural network-based program for predicting protein secondary structure sequence residues are assigned to one of three secondary-structure elements (alpha helix, beta sheet, or random coil). 

There are no current structural data of polyester synthases. The secondary structure content was inferred by predictions implementing the multiple alignments of synthases. The use of JPred indicated that polyester synthases are mostly composed of variable loops (49.7%) and a-helical (39.9%) secondary structures, whereas only 10.4% were proposed as P-sheet secondary structures [38]. However, circular dichroism spectroscopy suggested that the class II synthase from P. aeruginosa is comprised of the secondary structures 10% a-helix, 50% P-sheet, and 40% random coil [39]. 

Here refers to the number of residues actually considered for every prediction, (cons JPRED consensus prediction dsc DSC mul MULPRED nnssp NNSSP orig phd PhD in its most current implementation phd PhD as run by JPRED pred PREDATOR psipred PSIPRED zpred ZPRED). Q3 refers to the three-state accuracy of a given prediction. 

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