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Related Experiment Videos

LoopX: A Graphical User Interface-Based Database for Comprehensive Analysis and Comparative Evaluation of Loops from

Rajashekar Varma Kadumuri1, Ramakrishna Vadrevu1

  • 1Department of Biological Sciences, Birla Institute of Technology & Science-Pilani , Hyderabad, India .

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|April 5, 2017
PubMed
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Protein loop design is crucial for novel functions and stability. LoopX is a new database and tool that analyzes and compares protein loops for sequence and structural compatibility, aiding in protein engineering.

Area of Science:

  • Protein engineering and structural biology.
  • Bioinformatics and computational biology.

Background:

  • Protein loops are critical for protein function, folding, and stability.
  • Designing or modifying protein loops is a key strategy for creating novel functionalities and enhancing protein properties.

Purpose of the Study:

  • To develop a comprehensive database and user-friendly server, LoopX, for analyzing and comparing protein loops.
  • To facilitate the extraction and comparison of loops based on sequence and structural compatibility for protein design.

Main Methods:

  • Compiled a library of ~700,000 loops from protein structures, including sequence and conformational features.
  • Developed a graphical user interface with diverse query tools, search algorithms, and visualization options.
  • Incorporated novel features for analyzing polar/nonpolar environment and residue conservation within loops.
Keywords:
data miningdatabaseloop engineering/graftingprotein loopsweb-based GUI

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Main Results:

  • LoopX provides detailed sequence and structural information, including hydrogen bonding patterns and dihedral angles.
  • The server enables efficient searching and retrieval of compatible loops based on user-defined criteria.
  • New search functionalities enhance the identification of suitable loops for specific protein engineering targets.

Conclusions:

  • LoopX serves as a valuable database and visualization tool for protein loop analysis.
  • The server aids researchers in extracting and comparing candidate loops for protein design and engineering applications.
  • LoopX facilitates the development of novel proteins with improved stability and foldability.