FDA approved drugs complexed to their targets: evaluating pose prediction accuracy of docking protocols.

Journal of Molecular Modeling
Mohammed H Bohari, G Narahari Sastry

Abstract

Efficient drug discovery programs can be designed by utilizing existing pools of knowledge from the already approved drugs. This can be achieved in one way by repositioning of drugs approved for some indications to newer indications. Complex of drug to its target gives fundamental insight into molecular recognition and a clear understanding of putative binding site. Five popular docking protocols, Glide, Gold, FlexX, Cdocker and LigandFit have been evaluated on a dataset of 199 FDA approved drug-target complexes for their accuracy in predicting the experimental pose. Performance for all the protocols is assessed at default settings, with root mean square deviation (RMSD) between the experimental ligand pose and the docked pose of less than 2.0 Å as the success criteria in predicting the pose. Glide (38.7 %) is found to be the most accurate in top ranked pose and Cdocker (58.8 %) in top RMSD pose. Ligand flexibility is a major bottleneck in failure of docking protocols to correctly predict the pose. Resolution of the crystal structure shows an inverse relationship with the performance of docking protocol. All the protocols perform optimally when a balanced type of hydrophilic and hydrophobic interaction or dominant hydrophilic i...Continue Reading

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Citations

Mar 27, 2015·Journal of Molecular Recognition : JMR·Elizabeth YurievPaul A Ramsland
Dec 1, 2017·SAR and QSAR in Environmental Research·S JanardhanG Narahari Sastry
Jun 13, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Chang WenJun Xu
Feb 6, 2019·BMC Bioinformatics·Piyush AgrawalGajendra P S Raghava
Mar 12, 2013·Expert Review of Clinical Pharmacology·Naiem T IssaSivanesan Dakshanamurthy
Feb 6, 2020·Japanese Journal of Infectious Diseases·Yu KakuShuzo Matsushita
Apr 4, 2021·Journal of Biomolecular Structure & Dynamics·Nandan KumarG Narahari Sastry
Jan 24, 2018·The Journal of Physical Chemistry. B·Xing CheYi Qin Gao
Sep 2, 2021·Molecular Diversity·Sita Sirisha MadugulaG Narahari Sastry

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