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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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PPS: A computing engine to find Palindromes in all Protein sequences.

Zameer Ahmed1, Manickam Gurusaran1, Prasanth Narayana1

  • 1Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560 012, India.

Bioinformation
|February 12, 2014
PubMed
Summary

This study introduces PPS, a novel computing engine for identifying palindromic sequences and Single Amino Acid Repeats (SAARs) in proteins. It enables detailed analysis of these unique protein structures and their functions.

Keywords:
PalindromesSingle Amino Acid Repeatscomputing enginethree-dimensional crystal structures

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Area of Science:

  • Protein bioinformatics
  • Molecular biology
  • Structural biology

Background:

  • Protein primary structure consists of amino acid chains.
  • Palindromic sequences and Single Amino Acid Repeats (SAARs) are unique functional elements within proteins.
  • Detailed investigation of palindromic sequences in proteins remains limited.

Purpose of the Study:

  • To develop a computational tool for analyzing palindromic sequences and SAARs in protein databases.
  • To provide insights into the structure, function, and evolution of these unique protein motifs.
  • To create a user-friendly platform for researchers to explore these sequences.

Main Methods:

  • Development of the Protein Palindrome Server (PPS) computing engine.
  • Integration with protein sequence databases for comprehensive searching.
  • Utilizing Jmol for visualization of three-dimensional protein structures.

Main Results:

  • The PPS server allows users to search for occurrences of palindromes and SAARs.
  • It facilitates the visualization of protein structures associated with these sequences.
  • The server is the first of its kind, offering a unique resource for protein analysis.

Conclusions:

  • The PPS server provides a valuable resource for studying palindromic sequences and SAARs.
  • Enhanced understanding of these motifs can contribute to protein structure-function relationship studies.
  • The tool is freely accessible, promoting broader research in protein sequence analysis.