Design and application of PDBlib, a C++ macromolecular class library

Area of Science:

• * Computational Biology
• * Structural Biology
• * Bioinformatics

Background:

• * Biological macromolecule structures are crucial for understanding biological function.
• * Existing methods for representing and analyzing these structures can be limited.
• * A flexible and extensible software library is needed for advanced structural analysis.

Purpose of the Study:

• * To introduce PDBlib, an object-oriented C++ class library for representing 3D biological macromolecule structures.
• * To describe the library's design, features, and applications.
• * To provide a memory-resident structure representation independent of Protein Data Bank (PDB) file formats.

Main Methods:

• * Development of an extensible object-oriented class library in C++.
• * Organization of classes into categories for macromolecule modeling, extensibility, navigation, and file loading.
• * Implementation of general-purpose procedures for retrieving structural features.
• * Creation of applications like PDBtool and PDBview using the library.

Main Results:

• * PDBlib version 1.0 represents proteins, DNA, RNA, and complexes at PDB entry detail.
• * The library provides a memory-resident representation independent of PDB format, allowing data from various sources.
• * Developed applications include PDBtool for structure verification and PDBview for hardware-independent structure rendering.
• * Ongoing work focuses on data persistence and querying capabilities with MMQLlib.

Conclusions:

• * PDBlib offers a robust and extensible framework for representing and analyzing biological macromolecule structures.
• * The library facilitates the development of specialized bioinformatics tools.
• * Future enhancements aim to improve data management and querying for structural biology research.