Protein modeling and analysis of protein –ligand interaction The X-ray crystallography and NMR are experimental methods for develop 3D structures of bimolecular drug targets. In parallel, information about the structural dynamics and electronic properties about ligands has also increased. This has encouraged the rapid development of the structure-based drug design. Computational techniques such as docking and molecular dynamics studies with analysis of protein-ligand interaction are useful in drug design. QSAR and Structure Based Drug Designing The biological activity of molecules is usually measured in assays to establish the level of inhibition of particular signal transduction or metabolic pathways. Chemicals can also be biologically active by being toxic. Drug discovery often involves the use of QSAR to identify chemical structures that could have good inhibitory effects on specific targets and have low toxicity (non-specific activity). Structure-based drug design relies on knowledge of the three dimensional structure of the biological target. If an experimental structure of a target is not available, it may be possible to create a homology model of the target based on the experimental structure of a related protein. Using the structure of the biological target, candidate drugs that are predicted to bind with high affinity and selectivity to the target may be designed using interactive graphics and the intuition of a medicinal chemist. Alternatively various automated computational procedures may be used to suggest new drug candidates. DNA and Protein Sequences Analysis The sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Comparative analysis of biological sequence data and predication of structure-function relationship between bio molecules are useful for identification of new drug target and novel inhibitor design.