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Soumendranath Bhakat - Publications

Affiliations: 
2015-2020 Biophysics Lund University, Lund, Skåne län, Sweden 
 2021- Biochemistry and Biophysics Washington University School of Medicine, St. Louis, MO, United States 
Area:
enhanced sampling, molecular dynamics, biophysics
Website:
https://cbiores.com
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37 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Vats S, Bobrovs R, Söderhjelm P, Bhakat S. AlphaFold-SFA: Accelerated sampling of cryptic pocket opening, protein-ligand binding and allostery by AlphaFold, slow feature analysis and metadynamics. Plos One. 19: e0307226. PMID 39190764 DOI: 10.1371/journal.pone.0307226  0.692
2023 Meller A, Bhakat S, Solieva S, Bowman GR. Accelerating Cryptic Pocket Discovery Using AlphaFold. Journal of Chemical Theory and Computation. PMID 36948209 DOI: 10.1021/acs.jctc.2c01189  0.599
2022 Polino AJ, Miller JJ, Bhakat S, Mukherjee S, Bobba S, Bowman GR, Goldberg DE. The nepenthesin insert in the Plasmodium falciparum aspartic protease plasmepsin V is necessary for enzyme function. The Journal of Biological Chemistry. 102355. PMID 35952758 DOI: 10.1016/j.jbc.2022.102355  0.52
2022 Bhakat S, Söderhjelm P. Flap Dynamics in Pepsin-Like Aspartic Proteases: A Computational Perspective Using Plasmepsin-II and BACE-1 as Model Systems. Journal of Chemical Information and Modeling. 62: 914-926. PMID 35138093 DOI: 10.1021/acs.jcim.1c00840  0.659
2022 Bhakat S, Söderhjelm P. Flap Dynamics in Pepsin-Like Aspartic Proteases: A Computational Perspective Using Plasmepsin-II and BACE-1 as Model Systems Journal of Chemical Information and Modeling. 62: 914–926. DOI: https://doi.org/10.1021/acs.jcim.1c00840  0.33
2021 Bhakat S. Pepsin-like aspartic proteases (PAPs) as model systems for combining biomolecular simulation with biophysical experiments. Rsc Advances. 11: 11026-11047. PMID 35423571 DOI: 10.1039/d0ra10359d  0.421
2021 Bhakat S. Pepsin-like aspartic proteases (PAPs) as model systems for combining biomolecular simulation with biophysical experiments Rsc Advances. 11: 11026-11047. DOI: 10.1039/D0RA10359D  0.323
2017 Bhakat S, Åberg E, Söderhjelm P. Prediction of binding poses to FXR using multi-targeted docking combined with molecular dynamics and enhanced sampling. Journal of Computer-Aided Molecular Design. PMID 29052792 DOI: 10.1007/S10822-017-0074-X  0.714
2017 Bhakat S, Söderhjelm P. 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: 119-132. PMID 27573983 DOI: 10.1007/S10822-016-9948-6  0.669
2016 Moonsamy S, Bhakat S, Ramesh M, Soliman ME. Identification of Binding Mode and Prospective Structural Features of Novel Nef Protein Inhibitors as Potential Anti-HIV Drugs. Cell Biochemistry and Biophysics. PMID 27981421 DOI: 10.1007/S12013-016-0774-1  0.543
2016 Moonsamy S, Bhakat S, Walker RC, Soliman ME. Single Active Site Mutation Causes Serious Resistance of HIV Reverse Transcriptase to Lamivudine: Insight from Multiple Molecular Dynamics Simulations. Cell Biochemistry and Biophysics. 74: 35-48. PMID 26972300 DOI: 10.1007/S12013-015-0709-2  0.538
2016 Mahanti M, Bhakat S, Nilsson UJ, Söderhjelm P. Flap Dynamics in Aspartic Proteases: A Computational Perspective. Chemical Biology & Drug Design. 88: 159-77. PMID 26872937 DOI: 10.1111/Cbdd.12745  0.716
2016 Thakur A, Dan N, Bhakat S, Jayaprakash V, Banerjee S. 5' Adenosine Monophosphate-Activated Protein Kinase Modulators as Anticancer Agents. Anti-Cancer Agents in Medicinal Chemistry. PMID 26863881 DOI: 10.2174/1871520616666160211124240  0.361
2016 Abhinand PA, Shaikh F, Bhakat S, Radadiya A, Bhaskar LV, Shah A, Ragunath PK. Insights on the structural perturbations in human MTHFR Ala222Val mutant by protein modeling and molecular dynamics. Journal of Biomolecular Structure & Dynamics. 34: 892-905. PMID 26273990 DOI: 10.1080/07391102.2015.1057866  0.497
2016 Kumalo HM, Bhakat S, Soliman ME. Investigation of flap flexibility of β-secretase using molecular dynamic simulations. Journal of Biomolecular Structure & Dynamics. 34: 1008-19. PMID 26208540 DOI: 10.1080/07391102.2015.1064831  0.499
2016 Thakur A, Dan N, Bhakat S, Jayaprakash V, Banerjee S. 5' adenosine monophosphate-activated protein kinase modulators as anticancer agents Anti-Cancer Agents in Medicinal Chemistry. 16: 961-972. DOI: 10.2174/1871520616666160211124240  0.268
2015 Moonsamy S, Bhakat S, Soliman ME. Dynamic features of apo and bound HIV-Nef protein reveal the anti-HIV dimerization inhibition mechanism. Journal of Receptor and Signal Transduction Research. 35: 346-56. PMID 26355431 DOI: 10.3109/10799893.2014.984310  0.512
2015 Bhakat S. Effect of T68A/N126Y mutations on the conformational and ligand binding landscape of Coxsackievirus B3 3C protease. Molecular Biosystems. 11: 2303-11. PMID 26077945 DOI: 10.1039/C5Mb00262A  0.545
2015 Kumalo HM, Bhakat S, Soliman ME. Heat-shock protein 90 (Hsp90) as anticancer target for drug discovery: an ample computational perspective. Chemical Biology & Drug Design. 86: 1131-60. PMID 25958815 DOI: 10.1111/Cbdd.12582  0.434
2015 Bhakat S, Soliman ME. Chikungunya virus (CHIKV) inhibitors from natural sources: a medicinal chemistry perspective. Journal of Natural Medicines. 69: 451-62. PMID 25921858 DOI: 10.1007/S11418-015-0910-Z  0.416
2015 Dan N, Bhakat S. 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: 324-48. PMID 25827401 DOI: 10.1016/J.Ejmech.2015.03.049  0.448
2015 Chetty S, Bhakat S, Martin AJ, Soliman ME. 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. 1-17. PMID 25671669 DOI: 10.1080/07391102.2015.1018326  0.535
2015 Kumalo HM, Bhakat S, Soliman ME. Theory and applications of covalent docking in drug discovery: merits and pitfalls. Molecules (Basel, Switzerland). 20: 1984-2000. PMID 25633330 DOI: 10.3390/Molecules20021984  0.495
2015 Karubiu W, Bhakat S, McGillewie L, Soliman ME. Flap dynamics of plasmepsin proteases: insight into proposed parameters and molecular dynamics. Molecular Biosystems. 11: 1061-6. PMID 25630418 DOI: 10.1039/C4Mb00631C  0.447
2015 Nayak BV, Ciftci-Yabanoglu S, Bhakat S, Timiri AK, Sinha BN, Ucar G, Soliman MES, Jayaprakash V. Monoamine oxidase inhibitory activity of 2-aryl-4H-chromen-4-ones Bioorganic Chemistry. 58: 72-80. PMID 25506816 DOI: 10.1016/J.Bioorg.2014.11.008  0.401
2015 Maharaj Y, Bhakat S, Soliman MES. 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 & Discovery. 12: 302-313. DOI: 10.2174/1570180811666141001005536  0.424
2015 Abhinand PA, Shaikh F, Bhakat S, Radadiya A, Bhaskar LVKS, Shah A, Ragunath PK. Insights on the structural perturbations in human MTHFR Ala222Val mutant by protein modeling and molecular dynamics Journal of Biomolecular Structure and Dynamics. DOI: 10.1080/07391102.2015.1057866  0.383
2015 Bhakat S, Delang L, Kaptein S, Neyts J, Leyssen P, Jayaprakash V. 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. DOI: 10.1039/C5Ra14469H  0.457
2015 Moonsamy S, Bhakat S, Walker RC, Soliman MES. Single Active Site Mutation Causes Serious Resistance of HIV Reverse Transcriptase to Lamivudine: Insight from Multiple Molecular Dynamics Simulations Cell Biochemistry and Biophysics. DOI: 10.1007/s12013-015-0709-2  0.395
2014 Bhakat S, Karubiu W, Jayaprakash V, Soliman ME. 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. PMID 25305334 DOI: 10.1016/J.Ejmech.2014.10.010  0.45
2014 Karubiu W, Bhakat S, Soliman ME. Compensatory role of double mutation N348I/M184V on nevirapine binding landscape: insight from molecular dynamics simulation. The Protein Journal. 33: 432-46. PMID 25107349 DOI: 10.1007/S10930-014-9576-8  0.493
2014 Bhakat S, Martin AJ, Soliman ME. 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: 2215-28. PMID 24931725 DOI: 10.1039/C4Mb00253A  0.51
2014 Shaikh F, Bhakat S, Thakur A, Radadiya A, Soliman MES, Shah A. Identification of Novel GSK1070916 Analogs as Potential Aurora B Inhibitors: Insights from Molecular Dynamics and MM/GBSA Based Rescoring Letters in Drug Design & Discovery. 12: 2-13. DOI: 10.2174/1570180811666140725184953  0.465
2014 Bhakat S, Karubiu W, Jayaprakash V, Soliman MES. 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. DOI: 10.1016/j.ejmech.2014.10.010  0.373
2014 Bhakat S, Shaikh F, Yadav S, Rawal RM. Identification of neuraminidase inhibitors by structure-based screening: promising new leads for influenza Medicinal Chemistry Research. 23: 2803-2809. DOI: 10.1007/S00044-013-0862-3  0.387
2011 Bhakat S. The ERC Mechanism and the Formation of Abnormal Product in the Stevens Rearrangement Volume 10, Issue 3. 10. DOI: 10.33697/AJUR.2011.018  0.227
2011 Bhakat S. ChemInform Abstract: The Controversial Reaction Mechanism of Stevens Rearrangement Cheminform. 42: no-no. DOI: 10.1002/chin.201141275  0.187
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