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Arghya Barman, Ph.D. - Publications

Affiliations: 
2012 Chemistry University of Miami, Coral Gables, FL 
Area:
Biochemistry, General Biophysics
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24 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
2016 Paul TJ, Barman A, Ozbil M, Bora RP, Zhang T, Sharma G, Hoffmann Z, Prabhakar R. Mechanisms of peptide hydrolysis by aspartyl and metalloproteases. Physical Chemistry Chemical Physics : Pccp. 18: 24790-24801. PMID 27711373 DOI: 10.1039/C6Cp02097F  0.774
2016 Barman A, Hamelberg D. Coupled Dynamics and Entropic Contribution to the Allosteric Mechanism of Pin1. The Journal of Physical Chemistry. B. PMID 27077947 DOI: 10.1021/Acs.Jpcb.6B02123  0.307
2016 Barman A, Smitherman C, Souffrant M, Gadda G, Hamelberg D. Conserved Hydration Sites in Pin1 Reveal a Distinctive Water Recognition Motif in Proteins. Journal of Chemical Information and Modeling. 56: 139-47. PMID 26651388 DOI: 10.1021/Acs.Jcim.5B00560  0.327
2015 Barman A, Batiste B, Hamelberg D. Pushing the Limits of a Molecular Mechanics Force Field To Probe Weak CH···π Interactions in Proteins. Journal of Chemical Theory and Computation. 11: 1854-63. PMID 26574391 DOI: 10.1021/Ct501036R  0.332
2015 Liu F, Geng J, Gumpper RH, Barman A, Davis I, Ozarowski A, Hamelberg D, Liu A. An Iron Reservoir to the Catalytic Metal: THE RUBREDOXIN IRON IN AN EXTRADIOL DIOXYGENASE. The Journal of Biological Chemistry. 290: 15621-34. PMID 25918158 DOI: 10.1074/Jbc.M115.650259  0.332
2015 Zhang T, Ozbil M, Barman A, Paul TJ, Bora RP, Prabhakar R. Theoretical insights into the functioning of metallopeptidases and their synthetic analogues. Accounts of Chemical Research. 48: 192-200. PMID 25607542 DOI: 10.1021/Ar500301Y  0.771
2015 Barman A, Hamelberg D. Loss of intramolecular electrostatic interactions and limited conformational ensemble may promote self-association of cis-tau peptide. Proteins. 83: 436-44. PMID 25524218 DOI: 10.1002/Prot.24740  0.349
2015 Zhang T, Ozbil M, Barman A, Paul TJ, Bora RP, Prabhakar R. Theoretical insights into the functioning of metallopeptidases and their synthetic analogues Accounts of Chemical Research. 48: 192-200. DOI: 10.1021/ar500301y  0.656
2014 Barman A, Prabhakar R. Computational Insights into Substrate and Site Specificities, Catalytic Mechanism, and Protonation States of the Catalytic Asp Dyad of β -Secretase. Scientifica. 2014: 598728. PMID 25309776 DOI: 10.1155/2014/598728  0.7
2014 Barman A, Hamelberg D. Cysteine-mediated dynamic hydrogen-bonding network in the active site of Pin1. Biochemistry. 53: 3839-50. PMID 24840168 DOI: 10.1021/Bi5000977  0.414
2013 Barman A, Prabhakar R. Elucidating the catalytic mechanism of β-secretase (BACE1): a quantum mechanics/molecular mechanics (QM/MM) approach. Journal of Molecular Graphics & Modelling. 40: 1-9. PMID 23337572 DOI: 10.1016/J.Jmgm.2012.12.010  0.715
2013 Choudhury R, Barman A, Prabhakar R, Ramamurthy V. Hydrocarbons depending on the chain length and head group adopt different conformations within a water-soluble nanocapsule: 1H NMR and molecular dynamics studies. The Journal of Physical Chemistry. B. 117: 398-407. PMID 23215251 DOI: 10.1021/Jp3090815  0.595
2012 Ozbil M, Barman A, Bora RP, Prabhakar R. Computational Insights into Dynamics of Protein Aggregation and Enzyme-Substrate Interactions. The Journal of Physical Chemistry Letters. 3: 3460-9. PMID 26290973 DOI: 10.1021/Jz301597K  0.765
2012 Barman A, Prabhakar R. Protonation states of the catalytic dyad of β-secretase (BACE1) in the presence of chemically diverse inhibitors: a molecular docking study. Journal of Chemical Information and Modeling. 52: 1275-87. PMID 22545704 DOI: 10.1021/Ci200611T  0.634
2012 Zhu X, Bora RP, Barman A, Singh R, Prabhakar R. Dimerization of the full-length Alzheimer amyloid β-peptide (Aβ42) in explicit aqueous solution: a molecular dynamics study. The Journal of Physical Chemistry. B. 116: 4405-16. PMID 22448932 DOI: 10.1021/Jp210019H  0.673
2012 Zhu X, Barman A, Ozbil M, Zhang T, Li S, Prabhakar R. Mechanism of peptide hydrolysis by co-catalytic metal centers containing leucine aminopeptidase enzyme: a DFT approach. Journal of Biological Inorganic Chemistry : Jbic : a Publication of the Society of Biological Inorganic Chemistry. 17: 209-22. PMID 21918843 DOI: 10.1007/S00775-011-0843-2  0.764
2011 Vetrivel KS, Barman A, Chen Y, Nguyen PD, Wagner SL, Prabhakar R, Thinakaran G. Loss of cleavage at β'-site contributes to apparent increase in β-amyloid peptide (Aβ) secretion by β-secretase (BACE1)-glycosylphosphatidylinositol (GPI) processing of amyloid precursor protein. The Journal of Biological Chemistry. 286: 26166-77. PMID 21642424 DOI: 10.1074/Jbc.M111.260471  0.627
2011 Barman A, Schürer S, Prabhakar R. Computational modeling of substrate specificity and catalysis of the β-secretase (BACE1) enzyme. Biochemistry. 50: 4337-49. PMID 21500768 DOI: 10.1021/Bi200081H  0.721
2011 Echeverria V, Zeitlin R, Burgess S, Patel S, Barman A, Thakur G, Mamcarz M, Wang L, Sattelle DB, Kirschner DA, Mori T, Leblanc RM, Prabhakar R, Arendash GW. Cotinine reduces amyloid-β aggregation and improves memory in Alzheimer's disease mice. Journal of Alzheimer's Disease : Jad. 24: 817-35. PMID 21321389 DOI: 10.3233/Jad-2011-102136  0.601
2010 Bora RP, Barman A, Zhu X, Ozbil M, Prabhakar R. Which one among aspartyl protease, metallopeptidase, and artificial metallopeptidase is the most efficient catalyst in peptide hydrolysis? The Journal of Physical Chemistry. B. 114: 10860-75. PMID 20669962 DOI: 10.1021/Jp104294X  0.74
2010 Echeverria V, Burgess S, Zeitlin R, Barman A, Thakur G, Inouye H, Feris E, Buckingham S, Kirschner D, Mori T, Leblanc R, Prabhakar R, Sattelle D, Arendash G. P3-290: Cotinine: A dual-action drug with multiple benefits against Alzheimer's disease Alzheimer's & Dementia. 6: S536-S537. DOI: 10.1016/J.Jalz.2010.05.1790  0.561
2009 Singh R, Barman A, Prabhakar R. Computational insights into aspartyl protease activity of presenilin 1 (PS1) generating Alzheimer amyloid beta-peptides (Abeta40 and Abeta42). The Journal of Physical Chemistry. B. 113: 2990-9. PMID 19708161 DOI: 10.1021/Jp811154W  0.687
2009 Barman A, Taves W, Prabhakar R. Insights into the mechanism of methionine oxidation catalyzed by metal (Cu(2+), Zn(2+), and Fe(3+)) - amyloid beta (Abeta) peptide complexes: A computational study. Journal of Computational Chemistry. 30: 1405-13. PMID 19037857 DOI: 10.1002/Jcc.21167  0.661
2009 Zhao Z, Singh R, Barman A, Johnson NF, Prabhakar R. Modeling the Self-Assembly Dynamics of Macromolecular Protein Aggregates Underlying Neurodegenerative Disorders Journal of Computational and Theoretical Nanoscience. 6: 1338-1351. DOI: 10.1166/Jctn.2009.1183  0.564
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