Online protein structure prediction

The computational studies on protein structures have been carried out from different perspectives in biology. These perspectives include 1) comparison of protein structures, 2) structural analysis, and 3) protein structure prediction. Table 1 lists the online resources that are providing such services. 

ExPASy Proteomics tools (http //expasy.org/tools/), tools and online programs for protein identification and characterization, similarity searches, pattern and profile searches, posttranslational modification prediction, topology prediction, primary structure analysis, or secondary and tertiary structure prediction. 

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). 

This chapter focuses on the application of molecular modeling to calculate, manipulate, and predict protein structures and functions. Concepts of structure similarity/ overlap, homology modeling, and molecular docking, which are special concerns of protein biochemists, are considered. Approaches to protein modeling by the use of two programs (Swiss-Pdb Viewer and KineMage) and two online servers (B and CE) are described. 

Table 1 Online resources for protein structure analysis and prediction...

TABLE 16.10 Online servers for predicting protein secondary structures... 

Knight, James D. R., Bin Qian, David Baker, and Rashmi Kothary. Conservation, Variability and the Modeling of Active Protein Kinases. Public Library of Science (PLoS) ONE, October 3, 2007. Available online. URL http //www.plosone.org/article/info%3Adoi%2Fl 0.1371%2 FJournal.pone.0000982. Accessed May 28,2009. The researchers compared some of the 518 known human protein kinases, and introduced an algorithm that may become useful in predicting their structures. 

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