Protein Function Prediction Using Protein Structure and Computational Methods

Abbasi Dezfouli, Mohammad Ebrahim | 2011

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  1. Type of Document: M.Sc. Thesis
  2. Language: Farsi
  3. Document No: 41560 (05)
  4. University: Sharif University of Technology
  5. Department: Electrical Engineering
  6. Advisor(s): Fatemizadeh, Emad; Arab, Shahriar
  7. Abstract:
  8. Predicting the Amino Acids that have a catalytic effect in the enzymes, is a big step in appointing the activity of the enzymes and classifying them. This is a very challenging job, because an Amino Acid can appear in a variety of active sites.The biological activity of a protein usually depends on the existence of a small number of Amino Acids. Detecting these Amino Acids from the sequence of Amino Acids has many applications. Usually, the Amino Acids that are preserved are known as the Amino Acids that build up the active site, but the algorithms for finding the preserved Amino Acids are much more complex. There are a lot of algorithms for predicting the active sites of Amino Acids, but only a small amount of these algorithms have been implemented for the public to use.In this project, we will introduce a tool for predicting the active sites that will use the spatial coordinates and the type of Amino Acids that contain the active sites.Implementation of this project will produce a database that consists of information about the enzymes and the kind of activity and the specifications of the active site of enzymes. This data can be accessed directly or used to identify the Function and the place of the active site of a query protein.This capability of the program can increase our knowledge about the available enzymes. Also it can be used for the proteins that their structure is known but we have no information about their function.The database has been produced from enzymes that have known active sites and have been referenced in literature. These data can be retrieved by entering the protein code. Also the program can detect the active site and in conclusion, the function of the protein in a query protein using the structure of the protein and the PDB code. This program is useful in understanding the activity of enzymes and also in designing new enzymes.In the first step of this project, we will gather the active site data and construct a database containing the data from different enzymes, the type of activity, the Amino Acids involved in the active site, the chain ID and the Residue number of the Amino Acids.Afterwards, an algorithm for searching these active sites will be implemented. The algorithm will use structure comparing to search the query protein to find the most similar zone to the active sites and will return these zones and the corresponding RMSD that was calculated. If this search is done over all the active sites in the database, we can rank the found sites according to similarity and find the activity of the enzyme.
  9. Keywords:
  10. Protein Function Prediction ; Protein Structure ; Computational Method ; Subgraph Isomorphism

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