Publications

Google Scholar [LINK]

Preprints

Bhakat, S. and Soderhjelm, P. (2022) Computational modelling of local fluctuations causing transient solvent exposure of protein amides, bioRxiv, LINK, Software, Github

Meller, A, Bhakat, S*, Solieva, S, and Bowman R.G* (2023) Accelerating cryptic pocket discovery using AlphaFold, bioRxiv, LINK, Github

Selected Journal Articles

Polino, J.A, Miller J.J, Bhakat, S, Mukherjee, S, Bobba, S, Bowman R. G, Goldberg, E. D. (2022) The nepenthesin insert in Plasmodium falciparum aspartic protease plasmepsin V is necessary for enzyme function, Journal of Biological Chemistry, LINK, Github

Bhakat, S*. and Soderhjelm, P. (2022)  Flap dynamics in pepsin-like aspartic proteases: a computational perspective using Plasmepsin-II and BACE-1 as model systems, Journal of Chemical Information and Modelling, 2022, 62, 4, 914–926, LINK, Github

Bhakat, S., Soderhjelm P. (2017) 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, 31(1):119-132, LINK

Bhakat, S., Aberg, E., and Soderhjelm, P. (2018) Prediction of binding poses to FXR using multi-targeted docking combined with molecular dynamics and enhanced sampling, Journal of Computer-Aided Molecular Design, 32(1):59-73, LINK

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

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, 5, 85938-85949, LINK

Karubiu, W., Bhakat, S., and Soliman, M.E. (2015) Flap Dynamics of Plasmepsin Proteases: Proposed Parameters and Molecular Dynamics Insight, Molecular Biosystems, 11, 1061-1066, LINK

Bhakat, S. (2015) Effect of T68A/N126Y mutations on conformational and ligand binding landscape of Coxsackievirus B3 3C protease, Molecular Biosystems, 11, 2303-2311, LINK

 

Critical Reviews

Bhakat, S. (2022) Collective variable discovery in the age of machine learning: reality, hype and everything in between, RSC Advances, 12, 25010 25024 LINK

Bhakat, S. (2021) Pepsin-like aspartic proteases (PAPs) as model systems for combining biomolecular simulation with biophysical experiments, RSC Advances, 11, 11026-11047, LINK, Github

 

Reviews

Mahanti M., Bhakat, S., Nilsson, U.J., Soderhjelm, P. (2016)  Flap Dynamics in Aspartic Proteases: A computational perspective, Chemical Biology and Drug Design, 88(2):159-77, LINK

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

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

Khumalo, H., Bhakat, S., Soliman, M.E. (2015)  Covalent Molecular Docking in Drug Design: Merits and Pitfalls”, Molecules, 20, 1984-2000, LINK