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Design and application of a C++ macromolecular class library
W Chang1, I N Shindyalov, C Pu
1Dept. of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10032, USA.
Proceedings. International Conference on Intelligent Systems for Molecular Biology
|January 1, 1994
Summary
PDBlib is a C++ class library for representing 3D biological macromolecular structures. It enables knowledge discovery from structural data and supports various applications for querying and visualizing protein, DNA, and RNA structures.
Area of Science:
- Computational Biology
- Structural Bioinformatics
- Software Engineering
Background:
- Representing and analyzing 3D macromolecular structures is crucial for biological knowledge discovery.
- Existing methods for handling structural data can be limited in flexibility and data source integration.
Purpose of the Study:
- To introduce PDBlib, an object-oriented C++ library for representing macromolecular structures.
- To detail the software design, usage, and applications of PDBlib within a larger knowledge discovery framework.
Main Methods:
- Developed an extensible, object-oriented C++ class library (PDBlib) for macromolecular structure representation.
- Ensured memory resident representation is independent of Protein Data Bank (PDB) format, allowing diverse data back-ends.
- Created prototype applications: Macromolecular Query Language (MMQL), PDBtool, and PDBview.
Main Results:
- PDBlib accurately represents structural features of proteins, DNA, RNA, and complexes.
- The library integrates with various data sources, including relational and object-oriented databases.
- Prototype applications demonstrate PDBlib's utility for querying, verification, and rendering of macromolecular structures.
Conclusions:
- PDBlib provides a flexible and robust foundation for computational analysis of macromolecular structure data.
- The library and associated tools facilitate advanced knowledge discovery from structural biology datasets.
- Software is publicly available for broader research community adoption.