Docking
- 1. Molecular Docking And Computer Aided Drug Design PILLAI ASWATHY VISWANATH BOTANY
- 2. Molecular docking can be defined as the binding of small molecule called ligand, on to a specific site in a larger molecule
- 3. Docking is a structure-based technique which attempts to find the “best” match, between two molecules.
- 4. In the field of molecular modeling, docking is a method which predicts the preferred orientation of one molecule to a second when bound to each other to form a stable complex. Knowledge of the preferred orientation in turn may be used to predict the strength of association or binding affinity between two molecules
- 5. In bioinformatics,molecular docking analyses are done to identify chemical that are able to interact and form stable complexes with target proteins To do this , the structure of both the ligand and the target protein should be known, so that docking can be simulated in a computer
- 6. The protein targets and the ligands are modeled using appropriate modeling software The docking software then simulates the binding of the ligand to target and calculates the energy levels of each such interaction in different orientations
- 7. It then applies thermodynamic principle and energy minimization algorithms to identify the molecules that form the best fit The best fitting molecule is one which gives structural and chemical stability to the ligand-target complex The ligand will thus form an ideal candidate for drug development Molecular docking is a key tool used in Computer Aided Drug Design
- 8. COMPUTER AIDED DRUG DESIGN The drug is most commonly an organic small molecule that activates or inhibits the function of a biomolecule such as a protein , which in turn results in a therapeutic benefit to the pateint Drug design is the inventive process of finding new medications based on the knowledge of the biological target The designing of a drug involves design of small molecules that are complementary in shape and charge to the biomolecular target to which they interact and there fore will bind to it
- 9. Drug designing is essentially the designing of appropriate ligand Computer aided drug designing is a practical and realistic way of helping the medical chemist and leads to pharmaceutical Ther are two major types of drug design: ligand based drug design structure based drug design
- 11. LIGAND BASED DRUG DESIGN This is based on the knowledge of other molecules Here,the new drug is designed according to the structure of naturally occuring ligand or form a drug or compound that is already in use Most often the drugs thus invented have spatial characteristic that are complementary to their target site that enable them to bind to their target.
- 13. STRUCTURE BASED DRUG DESIGN Based on the structure of the target,drugs are designed in such a way that these have a complementary structure that fits stably in to their target This is done by using interactive graphics that identifies the complementary structure that has a high affinity to the target As mentioned earlier, drug designing is also useful in modifying existing drugs or drugs that have been identified by computer aided drug discovery to improve upon their efficiency