PDBTool: A Prototype Object Oriented Toolkit for Protein Structure Verification

Abstract

The Protein Data Bank (PDB) is a large and rapidly growing standard repository of complex biological macromolecules. Existing software tools for the PDB, including storage management, are quite inflexible and work in isolation. We are using object-oriented design and object-oriented database techniques in the construction of a toolbox for the PDB. The main components of the object- oriented toolbox include: (1) a uniform graphical user interface for fast, intuitive, and interactive access to the PDB; (2) several interoperable storage managers. compatible with present and future PDB formats; (3) a new set of efficient, modular, and flexible software tools. The toolbox is being implemented in C(++). We describe our experience in the implementation and use of the first prototype, PDBTool, to display, manipulate, and verify the structure of proteins. This project is a successful collaboration of a Biophysics and a Computer Science research and development team.

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Document Details

Document Type
Technical Report
Publication Date
Jan 01, 1992
Accession Number
ADA274501

Entities

People

  • A. S. Chang
  • C. Pu
  • Chang Liu
  • J. Ong
  • K. P. Sheka

Organizations

  • Columbia University

Tags

Communities of Interest

  • Advanced Electronics

DTIC Thesaurus Topics

  • Biochemistry
  • Biophysics
  • Chemistry
  • Computer Programming
  • Computer Science
  • Computers
  • Databases
  • Graphical User Interface
  • Molecular Biology
  • Mrna
  • Operating Systems
  • Relational Database Management Systems
  • Relational Databases
  • Ribonucleic Acids
  • Software Development
  • Teamwork
  • User Interface

Fields of Study

  • Computer science
  • Engineering

Readers

  • Database Systems and Applications
  • Molecular and Cellular Biochemistry

Technology Areas

  • Biotechnology