Publications

LIFE_art_show
Google Scholar [LINK]

Doctoral Student (July2015 contd.)

1. Bhakat S, Åberg E and Söderhjelm P (2017) Prediction of binding poses to FXR using multi-targeted docking combined with molecular dynamics and enhanced sampling, Journal of Computer-aided Molecular Design, [LINK]
2. Bhakat S, Söderhjelm P (2016) Resolving the problem of trapped water in binding cavities: Prediction of host-guest binding free energies in the SAMPL5 challenge by funnel metadynamics, Journal of Computer-aided Molecular Design, Accepted [LINK]
3. Mahanti M, Bhakat S, Nilsson UJ, Söderhjelm P (2016) Flap Dynamics across Proteases: A computational perspective, Chemical Biology and Drug Design, Accepted
4. Bhakat S, Delang L, Kaptein S, Neyts J, Leyssen P and Jayaprakash V (2015)  Reaching beyond HIV/HCV: Nelfinavir as a potential starting point for broad-spectrum protease inhibitors against dengue and chikungunya virus , RSC Advances, Accepted [LINK]
5. Thakur A, Dan N, Bhakat S, Jayaprakash V and Banerjee S (2016) 5′ Adenosine Monophosphate-Activated Protein Kinase Modulators as Anticancer Agents , Anti-cancer agents in medicinal chemistry [LINK
6. Suri Moonsamy, Bhakat S, Ramesh M and Soliman M E (2017) Identification of binding mode and prospective structural features of novel Nef protein inhibitors as potential anti-HIV drugs, Cell Biochemistry and Biophysics, 75(1), 49-64. [LINK]

Research Assistant (April 2015-July 2015)

7. Bhakat S (2015) Effect of T68A/N126Y mutations on conformational and ligand binding landscape of Coxsackievirus B3 3C protease, Molecular Biosystems, Accepted [LINK
8. Khumalo HM, Bhakat S¶, Soliman M.E (2015) Investigation of Flap Flexibility of β-Secretase Using Molecular Dynamic Simulations, Journal of Biomolecular Structure & Dynamics, Accepted, as co-first & co-corresponding author
9. Abhinand P.A., Shaikh F, Bhakat S, Bhaskar L.V.K.S., Shah A, Ragunath PK, (2015) Insights on the structural perturbations in Human MTHFR Ala222Val mutant by protein modelling and molecular dynamics, Journal of Biomolecular Structure & Dynamics, Accepted 

Masters study (December 2013-April 2015)

10. Bhakat S, Martin A and Soliman M.E. (2014) An Integrated Molecular Dynamics, Principal Component Analysis and Residue Interaction Network Approach Reveals the Impact of M184V Mutation on HIV Reverse Transcriptase Resistance to Lamivudine, Molecular Biosystems, 10, 2215-2228 [LINK]
11. Bhakat S, Karubiu W, Venkatesan J and Soliman M.E. (2014) A perspective on targeting non-structural proteins to combat Neglected Tropical Diseases: Dengue, West Nile and Chikungunya viruses, European Journal of Medicinal Chemistry, 87, 677-702 [LINK], Listed as one of the most downloaded articles in 2014/15 Read More
12. Moonsamy S., Bhakat S*. and Soliman M.E. (2014) Dynamic features of apo and bound HIV-Nef protein reveal the anti-HIV dimerization inhibition mechanism, Journal of Receptors and Signal Transduction, In Press [LINK]
13. Nayak B.V, Ciftci S.Y, Bhakat S*, Timri A.K, Sinha B.N, Ucar G, Soliman M.E, Devadasan V, Jayaprakash V (2014) Monoamine oxidase inhibitory activity of 2-aryl-4H-chromen-4-one, Bioorganic Chemistry, In Press [LINK]
14. Karubiu W, Bhakat S, and Soliman M.E. (2014) Compensatory role of Double Mutation N348I/M184V on Nevirapine Binding Landscape: Insight from Molecular Dynamics Simulations, The Protein Journal, 33(5):432-446 [LINK]
15. Shaikh F, Bhakat S*, Thakur A, Shah A, Soliman M. E., (2014) Identification of novel GSK1070916 Analogs as Potential Aurora B Inhibitors: Insights from Molecular Dynamics and MM/GBSA based rescoring, Letters in Drug Design and Discovery, 12, 2-13 [LINK]
16. Maharaj Y., Bhakat S. and Soliman, M.E (2014) Computer-aided identification of novel DprE1 inhibitors as potential anti-TB lead compounds: A hybrid virtual-screening and molecular dynamics approach, Letters in Drug Design and Discovery, In press [LINK]
17. Khumalo H, Bhakat S, Soliman M.E. (2015) Covalent Molecular Docking in Drug Design: Merits and Pitfalls, Molecules, 20, 1984-2000 [LINK]
18. Karubiu W, Bhakat S and Soliman M.E (2015) Flap Dynamics of Plasmepsin Proteases: Proposed Parameters and Molecular Dynamics Insight, Molecular Biosystems, Published online [LINK]
19. Moonsamy S, Bhakat S*, Walker R.C., Soliman M.E., (2015) Single Active Site Mutation Causes Serious Resistance of HIV Reverse Transcriptase to Lamivudine: Insight from Multiple Molecular Dynamics Simulations, Cell Biochemistry and Biophysics, Accepted
20. Bhakat S*, Chetty S*, Martin AJM and Soliman, M.E. (2015) Multi-drug Resistance Profile of PR20 HIV-1 Protease is attributed to Distorted Conformational and Drug Binding Landscape: Molecular Dynamics Insights, Journal of Biomolecular Structure & Dynamics – Accepted [LINK]
21. Dan N*, Bhakat S* (2015) New paradigm of an old target: an update on structural biology and current progress in drug design towards Plasmepsin II, European Journal of Medicinal Chemistry, 95, 324-348 [LINK], as co-first and corresponding author
22. Bhakat S, Soliman, M.E. (2015) Chikungunya Virus (CHIKV) Inhibitors from Natural Sources: A Medicinal Chemistry Perspective, Journal of Natural Medicines, Accepted, as co-corresponding author, [LINK]
23. Kumalo HM, Bhakat S and Soliman M. E. (2015) Heat Shock Protein 90 (Hsp90) as Anti-cancer Target for Drug Discovery: An Ample Computational Perspective, Chemical biology & Drug Design, Accepted [LINK]

Undergraduate study and before (2009-2013)

24. Bhakat S, Shaikh F, Yadav S and Rawal R (2014) Identification of neuraminidase inhibitors by structure-based screening: promising new leads for influenza, Medicinal Chemistry Research, 23(6), 2803-2809 [LINK]
25. Bhakat S and Vipperla B (2013) Designing and Computational Study of Some Novel Lamivudine Analogues as potential HIV-1 Reverse Transcriptase Inhibitors: Analysis of the binding interactions using QSAR, molecular docking and molecular dynamics simulation study, International Journal of Pharmacy and Pharmaceutical Sciences, 5(1), 367-373
26. Bhakat S (2012) An efficient FeSO4 mediated synthesis of methyl-4-(ethoxymethyl) benzoate and basic conformational analysis of the same using computational tools, Stanford Undergraduate Research Journal, 27-30 [LINK]
27. Bhakat S (2012) SAR and Pharmacophore Based Designing of Some Antimalarial and Antiretroviral Agents: An Internet Based Drug Design Approach, Der Pharma Chemica, 4(3), 1247-126 [LINK]
29.Bhakat S (2012) Designing of a New Anticancer Agent: An internet based drug design Approach, International Journal of drug design and Discovery, 3(4), 898-90
30. Bhakat S (2011) The ERC mechanism and the formation of abnormal product in the Stevens Rearrangement, American Journal of Undergraduate Research,10, 1-5
31. Bhakat S (2011) The controversial reaction mechanism of Stevens rearrangement: A review, Journal of Chemical and Pharmaceutical Research, 3, 115-121
* Authors contributed equally

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