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Structural Protein Function01:56

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Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
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Lemon: a framework for rapidly mining structural information from the Protein Data Bank.

Jonathan Fine1, Gaurav Chopra1

  • 1Department of Chemistry, Purdue University, West Lafayette, IN, USA.

Bioinformatics (Oxford, England)
|March 16, 2019
PubMed
Summary

The Lemon framework offers a fast, flexible C++ library with Python bindings to analyze the entire Protein Data Bank (PDB). It streamlines the generation of 3D structural features for computational biology research.

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Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Biomolecular structure analysis

Background:

  • The Protein Data Bank (PDB) is a crucial resource with over 140,000 biomolecular structures.
  • Current methods for extracting PDB features for benchmarking are manual, slow, and non-standardized.
  • There is a need for efficient, standardized tools to query 3D descriptors from the PDB.

Purpose of the Study:

  • To develop a standardized framework for analyzing biomolecular structures in the PDB.
  • To enable rapid querying and characterization of 3D structural features.
  • To facilitate the creation of custom benchmarking sets for computational biology methods.

Main Methods:

  • Developed the Lemon framework, a C++11 library with Python bindings.
  • Utilized the MacroMolecule Transmission Format for efficient PDB file parsing.
  • Implemented C++ lambda functions and Python bindings for user-defined analysis.

Main Results:

  • The Lemon framework can parse and characterize the entire PDB in under 10 minutes on multi-threaded hardware.
  • Provides a consistent workflow for selecting biomolecular interactions and computing 3D features.
  • Offers flexibility for custom analysis and categorization of PDB data.

Conclusions:

  • Lemon provides a one-stop solution for rapidly mining the PDB.
  • Enables efficient generation of structural biology features for research and software development.
  • Addresses the scarcity of standardized tools for PDB analysis.