Supercomputing Facility for Bioinformatics &
Computational Biology, IIT Delhi
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RASPD for Preliminary Screening of Drugs
The challenge for computer aided drug discovery is to achieve this specificity - with small molecule inhibitors - in binding to target proteins, at reduced cost and time while ensuring synthesizability, novelty of the scaffolds and proper ADMET profiles. RASPD is a computationally fast protocol for identifying good candidates for any target protein. The binding pocket of the input target protein is scanned for the number of hydrogen bond donors, acceptors, number of hydrophobic groups and number of rings. A QSAR type equation combines the afore-mentioned properties of the target protein and the candidate molecule and an estimate of the binding free energy is generated if the target protein were to complex with the candidate. The most interesting feature of this methodology is that it takes fraction of a second for calculating the binding affinities of the protein-candidate molecule complexes as opposed to several minutes in known art today for regular docking and scoring method, whereas the accuracy of this method in sorting good candidates is comparable with the conventional techniques. We have also created million molecules database. This database is prepared to include chemical formula, structure, topological index, number of hydrogen bond donors and acceptors, number of hydrophobic groups, number of rings, logP values for each of the million molecules. Scoring of 1 million small molecule database by RASPD method to identify hits for a particular protein target is also web enabled for free access at the same site.

Click here
to see 'How to Use Tool'.

Method A [Protein-Ligand Complex]
Method B [Protein 3D Structure Without Ligand]
Method C [Customized Dataset]
Method D [Customized Molecule]

Enter Ligand Id [Identifier]:

Step 2: Click on 'Submit' to submit your job

Click Here to retrive the current status of your job.

References :

G. Mukherjee and B. Jayaram, "A Rapid Identification of Hit Molecules for Target Proteins via Physico-Chemical Descriptors", Phys. Chem. Chem. Phys., 2013, 15, 9107-16.

Number of Hits since 2nd March 2010: 18639