Structural Bioinformatics: Computational Software and Databases for the Evaluation of Protein Structure


  • Ayisha Amanullah Jinnah University for Women, Karachi, Pakistan
  • Suad Naheed Jinnah University for Women, Karachi, Pakistan



Database, PDB, CATH, MMDB, SCOP, domain, protein-protein complex systems


Databases are the computerized platform where information is stored and can be retrieved easily by public users. Biological databases are the repositories of biological data. These biological data libraries contain facts and figures related to various disciplines of research including genomics, proteomics, microarray technology, metabolomics and phylogenetics. By using biological databases, a broad collection of essential biological information can be exploited ranging from function, structure and localization of gene, clinical consequences of mutation to similarity index among biological sequences and structures. Nowadays, different kinds of biological databases are available on the web. The present write up focuses on biological databases and bioinformatics tools for protein structure analysis. This review also aims to elaborate the searching schemes, available in different structural databases. The wide variety of different levels and types of information content related to 3D protein structures are available on web-based databases. Regarding the biological functions and 3D structures of various proteins, these databases provide a huge range of useful links, schematic diagrams as well as strategies for detailed analysis of proteins and other macromolecules structures. 3D structural illustration of proteins stored in structural databases is determined and visualized by X-ray crystallography, electron microscopy and NMR spectroscopy. On regular basis, a large number of protein structures are submitted by structural biologists, updated and curated by subject experts. Most familiar biological databases that store 3D protein and other macromolecules structures include, PDB, 3D Genomics, CATH, & SCOP. These databases contain valuable information of overall protein structures, domains and motif structures, protein-protein complex systems and complex of protein with other biomolecules.

Author Biographies

Ayisha Amanullah, Jinnah University for Women, Karachi, Pakistan

Department of Biotechnology, 

Suad Naheed, Jinnah University for Women, Karachi, Pakistan

Department of Biotechnology