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Small Molecules: Hit identification
Small Molecules: Hit-to-Lead optimization
Small Molecules: physicochemical properties
Small Molecules: ADME
Small Molecules: Toxicity
Small Molecules: Selectivity
Antibodies: Humanization and Optimization
Protein Modeling. Discovery
Protein Modeling: HERG binding
Protein Modeling: Albumin binding
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VIRTUAL LIBRARY SCREENING
Description: Finds the position of the small molecules from a virtual library in the active site of a given protein with the minimum value of the free binding energy and predicts the IC50 of these molecules.
Library: The library of compounds can be your own. Alternative way is that Quantum Pharmaceuticals will provide you for free with a virtual library. There are following sets:
450,000 – Synthetic compounds; 35,000 – Diversified set of synthetic compounds
50,000 – Natural compounds; 10,000 – Diversified set of natural compounds
5,000 – Super-diversified set from collection of 500,000 compounds
4,000 – Synthetic and natural scaffold compounds
Any compound from our virtual library can be purchased from Interbioscreen a leading discovery chemistry provider.
Requirements: The Library Screening requires 3D structures of a protein and small molecules (2D is also possible for small molecules). The position of the active site of the protein should be known. Protein structures can be downloaded from the Protein Data Bank, as well as from some other sources of 3D biological macromolecular structure data. The protein and small molecules structures should be uploaded with the .pdb format (or any standard formats like .hin, .mol2 etc.). The small molecules have to have not more then 25 flexible bonds each.
Output/Results:
You will receive a package of the .pdb files with coordinates of the docked small molecules and the table with the information as follows:
- Name - name of small molecule
- IC50 uMol/L - IC50 value
- E bind, kJ/mol - free binding energy
- E es, kJ/mol - electrostatic and solvation energy
- E vdw, kJ/mol - short range electrostatic and exchange and Van der Waals energies
- TdS, kJ/mol - entropy contribution
- E tor, kJ/mol - ligand internal energy change
- Charge, Mass, Flex.bonds - total charge, mass and number of flexible bonds of the small molecule
- Accuracy of the prediction: Absolute deviation – 8 kJ and relative deviation – 15% (see Proof of consept_IC50).