A molecular dynamics simulation is a physics-based approach for understanding atom level motion and interactions of bio-molecules using Newton’s physics. Molecular dynamics simulation helps to analyze molecular interactions between bio-molecules in a dynamic environment, to be much more accurate and mimics the interactions as would happen in a cellular atmosphere.
The structure and dynamics are the fundamental units to explore functional mechanism of biological macro-molecules. Molecular dynamics is a powerful tool to study the conformational, functional and structural integrity of protein targets. It enables detailed calculation of atomic structure, including radial distribution functions, bond angle distributions, coordination number distributions, principle component analysis and other structural features.
This aid to develop combinatorial drug formulation to combat the pathogenic condition with lesser toxicity. There are various network structure (Protein-drug, protein-Pathway, protein-Molecular functions and gene-disease associations) were built and analyzed to scrutinize the effective drug combinations.
The cumulative analysis of all these networks strongly suggests the appropriate bio-active compounds against desired targets. Enrichment of the protein networks leads to have insights on attributes such as molecular functions, pathways, disease association and cellular component localization.