Pharmacology Computational Biology

scientificprotocols authored about 3 years ago

Authors: Aarti Garg, Rupinder Tewari & Gajendra Raghava

Abstract

A web server, KiDoQ, has been developed to serve scientific community working in the field of designing inhibitors against Dihydrodipicolinate synthase (DHDPS), a potential drug target enzyme of a unique bacterial DAP/Lysine pathway. The server has employed the molecular docking and ligand based QSAR strategies to predict inhibitory activity value (Ki) of small compounds for DHDPS enzyme. The algorithm behind the server includes the docking of compounds to the active binding site of enzyme followed by QSAR modeling where, docking generated energy based scoring values (for the best conformer) are cascaded as input variables to QSAR based SVM model for prediction of Ki value. The QSAR model implemented on the server has been trained on the dataset of 23 inhbitors of DHDPS and predict the Ki value with correlation R/q2 values of 0.93/0.80 and MAE of 1.89.

Procedure

The server is available from http://crdd.osdd.net/raghava/kidoq.

The following steps are used to do prediction of Ki value for a submitted structure

  1. Type the above mentioned URL in your web browser.
  2. Click “Submit” button on the home page of the server. The home page of KiDoQ server is shown in Figure 1A.
  3. User is required to fill the submission form (Figure 1B)
  4. Use can draw the chemical structure using JME editor or paste/browse the structure file in mol/mol2 format
  5. If chemical structure is pasted or browsed, user is required to select the type of file format.
  6. Click the Run button to get the results.

Associated Publications

KiDoQ: using docking based energy scores to develop ligand based model for predicting antibacterials. Aarti Garg, Rupinder Tewari, and Gajendra PS Raghava. BMC Bioinformatics 11 (1) doi:10.1186/1471-2105-11-125

Author information

Aarti Garg, Institute of Microbial Technology, Sector-39A, Chandigarh, INDIA

Rupinder Tewari, Department of Biotechnology, Panjab University, Chandigarh, INDIA

Gajendra Raghava, Raghava's Group

Correspondence to: Gajendra Raghava ([email protected])

Source: Protocol Exchange (2010) doi:10.1038/protex.2010.206. Originally published online 10 December 2010.

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