PredictProtein server

Figure 12.9. Protein structure prediction with PHD. The amino acid sequence of chicken lysozyme precursor (147 amino acids) is submitted to PredictProtein server for PHD structure predictions. The returned e-mail reports protein class based on secondary structures, predicted secondary structure composition (%H, %E, and %L), residue composition, data interpretation, and predicted data in two levels (brief and normal of which the normal is shown). Search for the database can be performed by making choice(s) from the list(s) of pop-up box(es).

RostB,YachdavG,Liu J (2004)The PredictProtein server. Nucleic Adds Res 32 W321-W326... 

Rost, B., G. Yachdav, and J. Liu. 2004. The PredictProtein server. Nucleic Acids Res 32, Web Server Issue W321-6. 

The method of Rost and Sander (Rost and Sander, 1993), which combines neural networks with multiple sequence alignments known as PHD, is available from the PredictProtein (Rost, 1996) server of Columbia University (http //cubic.bioc. columbia.edu/predictprotein/). This Web site offers the comprehensive protein sequence analysis and structure prediction (Figure 12.8). For the secondary structure prediction, choose Submit a protein sequence for prediction to open the submission form. Enter e-mail address, paste the sequence, choose options, and then click the... 

PredictProtein Protein structure analysis Automatic sequence alignment, protein fold recognition, and secondary structure prediction web server 177 www.embl-heidelberg.de/predictprotein/... 

Figure 1.2. Anatomy of an E-mail message, with relevant components indicated. This message is an automated reply to a request for help file for the PredictProtein E-mail server.

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