Molecular Dynamics Simulations for Biological Systems

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Author(s): Prerna Priya (Bose Institute – Kolkata, India), Minu Kesheri (Banaras Hindu University, India), Rajeshwar P. Sinha (Banaras Hindu University, India)and Swarna Kanchan (Birla Institute of Technology and Science (BITS), India)
Copyright: 2016
Pages: 28
Source title: Biomedical Image Analysis and Mining Techniques for Improved Health Outcomes
Source Author(s)/Editor(s): Wahiba Ben Abdessalem Karâa (Taif University, Saudi Arabia & RIADI-GDL Laboratory, ENSI, Tunisia)and Nilanjan Dey (Department of Information Technology, Techno India College of Technology, Kolkata, India)
DOI: 10.4018/978-1-4666-8811-7.ch014

Keywords: Bioinformatics / Medical Information Science Reference / Medicine & Healthcare

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Abstract

Molecular dynamics simulation is an important tool to capture the dynamicity of biological molecule and the atomistic insights. These insights are helpful to explore biological functions. Molecular dynamics simulation from femto seconds to milli seconds scale give a large ensemble of conformations that can reveal many biological mysteries. The main focus of the chapter is to throw light on theories, requirement of molecular dynamics for biological studies and application of molecular dynamics simulations. Molecular dynamics simulations are widely used to study protein-protein interaction, protein-ligand docking, effects of mutation on interactions, protein folding and flexibility of the biological molecules. This chapter also deals with various methods/algorithms of protein tertiary structure prediction, their strengths and weaknesses.

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