Protein Structure Prediction

Proteins are the machines that drive cells and ultimately organisms. There are twenty different amino acids, which forms proteins and the order of these amino acids in the protein sequence dictates their three-dimensional structure. The protein structures are determined experimentally using X-ray crystallography or NMR. But out of a few lakh protein sequences, only about fifty thousand have experimentally known structures as some structures cannot be crystallized easily due to their limitations. Protein Structure Prediction (PSP) is one of the most challenging tasks of computational structural biology & chemistry and it is expressed as the prediction of protein tertiary structure from primary structure. The main purpose of PSP is to understand the function. If the protein misfolds, it may lead to neurodegenerative diseases like Alzheimer’s.

This PSP technique is based on Genetic Algorithms. The GA-based PSP is made as a grid service and executed on SOA based GARUDA grid. From the portal, the PSP grid services can be invoked and executed for a given protein molecule.

The PSP Portal is a user-friendly web portal for submitting Protein Structure Prediction jobs to GARUDA Grid. The Portal will facilitate the viewing the generated structure for the given protein.

Features

  • Users can input protein files in two ways:
  • Upload the protein file from local machine on the PSP server.
  • Create the protein file by supplying required parameters.
  • Run the PSP web services on Garuda clusters.
  • Download the results.
  • View the structure by Rasmol viewer given as a plugin.

Availability

Platforms and Browsers that support PSP Portal
Linux Platform Mozilla ver. 1.6 and above.
Firefox ver. 1.0.4 and above
Windows Platform Internet Explorer ver. 6.0.2 and above.
Firefox ver. 1.5.0.1 and above.
Solaris Platform Netscape ver. 6.2.3 and above.