HEX structure prediction tool.pptx

Hex is used as the docking and structure prediction tool it used to find docking value between the molecules.

1. HEX structure prediction Tool G.MANIMARAN 21PO24 I ST MSC BIOTECH

2. HEX Hex  is an interactive  protein docking  and  molecular superposition  program, written by  Dave Ritchie .  Hex  understands protein and DNA structures in PDB format, and it can also read small-molecule SDF files. As of December 2015, there have been over 40,000 downloads. Hex is an interactive molecular graphics program for calculating and displaying feasible docking modes of pairs of protein and DNA molecules.

3. Hex can also calculate protein and ligand docking It is the first protein docking program to be able to use modern graphics processor units(GPU) to Accelerate the calculation

4. Scoring functions Force field  – affinities are estimated by summing the strength of intermolecular  van der Waals  and  electrostatic  interactions between all atoms of the two molecules in the complex using a  force field Empirical  – based on counting the number of various types of interactions between the two binding partners.Counting may be based on the number of ligand and receptor atoms in contact with each other or by calculating the change in  solvent accessible surface area .

5. Knowledge-based  – based on statistical observations of intermolecular close contacts in large 3D databases (such as the  Cambridge Structural Database  or  Protein Data Bank ) which are used to derive  statistical  " potentials of mean force ".  Machine-learning  – Unlike these classical scoring functions, machine-learning scoring functions are characterized by not assuming a predetermined functional form for the relationship between binding affinity and the structural features describing the protein-ligand complex

6. DATABASES RECEPTOR DATABASES PDB LIGAND DATABASES PUBCHEM TREMBL CHEMBL

7. Graphical Features Solid models solid surfaces Dot surfaces Harmonic surfaces Projection Animation Lighting fog

8. example Omicron receptor and dasatinib drug

9. EXAMPLES

10. Docking control

11. D ocking

12. Result