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Molecular Dynamic Simulations
Molecular dynamic (MD) simulations is a method in which physical movements of atoms and molecules under given physiochemical conditions. MD is widely used in determining the thermodynamic properties of the given protein structure in complex with/without ligand in the presence of solvent at given pH, temperature and pressure. Through this method total potential energy of the given protein-ligand complex along with associated interaction energies can be calculated towards validating their association strength during the conformational changes.
Structure And Ligand Based Virtual Screening Studies
Virtual screening is a computational technique used in drug discovery research for screening of large chemical space for potential lead drug candidates towards a known drug target, typically an enzyme or a protein receptor. As the accuracy and correlation of this method of screening with experimental results is increased, the application of this technique is being highly appreciated in pharma industries towards screening enormous chemical space of over 1060 small chemical compounds. Based on the available knowledge regarding potential drug target/ligand, structure/ligand based virtual screening will be implemented either individually or in combination for identifying potential lead drug like compounds.
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Homology modeling is a computational modeling technique used for generating high resolution hypothetical proteins by using the evolutionarily related protein structure information. This method is highly valuable when the structure of the protein target is not known. Presently available softwares allow us to build therapeutically important drug targets with high accuracy and correlation with experimentally determined protein structures.
Most of the biological functions depends upon the protein-protein interactions, especially signal transduction mechanisms, which is the core of the entire interactomics system of any living cell. Many disease pathways such as cancer, undesired protein-protein interactions are the key factors towards malfunctioning of the cells. Most of the anti cancer drugs have been identified by blocking the protein-protein interacting pathway. Hence, studying the network pathways involving many protein interactions is crucial towards finding novel drug targets and studying the protein-ligand interactions which can specifically target a particular protein-protein interaction is vital for novel drug discovery.