Supercomputing Facility for Bioinformatics &
Computational Biology, IIT Delhi
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Drug Design Software and Tools


1. Sanjeevini

   A complete drug design software.

2. Binding Affinity Prediction of Protein-Ligand Server(BAPPL)

   Computes the binding free energy of a protein-ligand complex.

3. Binding Affinity Prediction of Protein-Ligand complex containing Zinc Server
    (BAPPL-Z)

   Computes the binding free energy of a metalloprotein-ligand complex containing zinc.
4. Drug-DNA Interaction Energy (PreDDICTA)
   Calculates the Drug-DNA interaction energy.
5. ParDOCK - Automated Server for Rigid Docking
   Predicts the binding mode of the ligand in receptor target site.

6. Active Site Prediction

7. Automated Version Of Active Site Prediction (AADS)

   Predicts 10 binding sites in a protein target and docks the uploaded ligand molecule    at all 10 sites predicted in an automated mode.
8. Non Redundant Database of Small Molecules
   Virtual high throughput screening of small molecules and their optimization into lead-   like candidates.
9. Lipinski Filters
   Checks whether a drug satisfies the 5 Lipinski rules.

10. Molecular Volume Calculator

   Calculates the volume of a molecule

11. DNA Sequence to Structure

   Generates double helical secondary structure of DNA using conformational parameters     taken from experimental fiber-diffraction studies.

12. Hydrogen Addition to Nucleic Acid
   Adds the hydrogen coordinates to the X-ray crystal structures of Nucleic acid

13. Hydrogen Addition to Protein
   Adds the hydrogen coordinates to the X-ray crystal structures of Protein

14. DNA Ligand Docking
   Rigid Docking predicts the binding mode of the ligand in the minor groove of DNA.

15. Wiener Index Calculator
   This tool is useful for calculating Wiener index.

16. RASPD for Preliminary Screening of Drugs
   This tool is useful for preliminary screening of ligand molecules based on physico-chemical properties of the ligand and the active site of the protein. This will predict binding energy of drug/target at a preliminary stage.

17. Transferrable Partial Atomic Charge Model - up to 4 bonds (TPACM4)
    This tool is used for assignment of partial atomic charge of small molecules.