Structural Bioinformatics

Structural biology is a branch of biology that investigates and studies the 3D structure of biological molecules and their complexes. Investigating and studying the structure of these molecules is necessary to understand their function and role in the cell. This is because a biological molecule’s structure determines and defines its function.Understanding how cell components function is crucial to developing more effective and successful treatments for illnesses.

Research in the structural biology branch started in 1953, when Watson and Crick discovered the double helix structure of DNA. This was followed by the determination of the 3D structure of the myoglobin protein in 1958. Nowadays, the 3D structure of biological macromolecules is determined in laboratories using techniques like X-ray crystallography, nuclear magnetic resonance (NMR), and electron microscopy. Structures determined this way comprise structural biology data.

Due to the massive increase in the number of structural data in recent years, researchers have turned to bioinformatics approaches to organize and analyze these data. The branch of bioinformatics that collects, stores, analyzes, and interprets structural data is called structural bioinformatics. Structural bioinformatics uses computer models created based on the basic principles of biology, chemistry, physics, and computer science. These models are used to answer questions about the 3D structure of biological macromolecules like proteins, RNA, and DNA. Utilizing the speed and accuracy of computers, structural bioinformatics can play a significant role in improving health research, particularly by accelerating drug development and design.

Structural bioinformatics’ main goal is to create models and methods for studying and analyzing structural data. As well as solving various biological problems, these methods will help improve our understanding of biological systems. In summary, the purpose of these methods can be categorized into one or more of the following topics: developing databases to collect and store data, visualization and comparison of structures, protein classification, structural analysis, structure prediction, and simulation.

The main topics of research in the field of structural bioinformatics are:

• Protein and RNA structure predictions from sequence
• Protein function prediction from structure or sequence
• Protein classification
• Molecular movement modeling
• Binding site prediction
• Binding site modeling
• Drug design
• Functional protein design

For more information, please refer to the following sources:

• Burkowski, F. (2008). Structural Bioinformatics: An Algorithmic Approach. In Structural Bioinformatics: An Algorithmic Approach. https://doi.org/10.1201/9781420011791
• Gu, J., & Bourne, P. E. (2009). Structural bioinformatics (Vol. 44). John Wiley & Sons.
• Punetha, A., Sarkar, P., Nimkar, S., Sharma, H., KNR, Y., & Nagaraj, S. (2018). Structural Bioinformatics: Life Through The 3D Glasses BT  – Bioinformatics: Sequences, Structures, Phylogeny (A. Shanker (ed.); pp. 191–253). Springer Singapore. https://doi.org/10.1007/978-981-13-1562-6_10

Samish, I., Bourne, P. E., & Najmanovich, R. J. (2015). Achievements and challenges in structural bioinformatics and computational biophysics. Bioinformatics, 31(1), 146–150. https://doi.org/10.1093/bioinformatics/btu769