| Year |
Citation |
Score |
| 2023 |
Serafim LF, Jayasinghe-Arachchige VM, Wang L, Rathee P, Yang J, Moorkkannur N S, Prabhakar R. Distinct chemical factors in hydrolytic reactions catalyzed by metalloenzymes and metal complexes. Chemical Communications (Cambridge, England). PMID 37366367 DOI: 10.1039/d3cc01380d |
0.315 |
|
| 2022 |
Serafim LF, Jayasinghe-Arachchige VM, Wang L, Prabhakar R. Promiscuous Catalytic Activity of a Binuclear : Peptide and Phosphoester Hydrolyses. Journal of Chemical Information and Modeling. 62: 2466-2480. PMID 35451306 DOI: 10.1021/acs.jcim.2c00214 |
0.363 |
|
| 2021 |
Hu Q, Jayasinghe-Arachchige VM, Prabhakar R. Degradation of a Main Plastic Pollutant Polyethylene Terephthalate by Two Distinct Proteases (Neprilysin and Cutinase-like Enzyme). Journal of Chemical Information and Modeling. PMID 33534993 DOI: 10.1021/acs.jcim.0c00797 |
0.326 |
|
| 2020 |
Juliano SA, Serafim LF, Duay SS, Heredia Chavez M, Sharma G, Rooney M, Comert F, Pierce S, Radulescu A, Cotten ML, Mihailescu M, May ER, Greenwood AI, Prabhakar R, Angeles-Boza AM. A Potent Host Defense Peptide Triggers DNA Damage and is Active against Multi-Drug Resistant Gram-Negative Pathogens. Acs Infectious Diseases. PMID 32251582 DOI: 10.1021/Acsinfecdis.0C00051 |
0.364 |
|
| 2020 |
Tolbert AE, Ervin CS, Ruckthong L, Paul TJ, Jayasinghe-Arachchige VM, Neupane KP, Stuckey JA, Prabhakar R, Pecoraro VL. Heteromeric three-stranded coiled coils designed using a Pb(II)(Cys) template mediated strategy. Nature Chemistry. PMID 32123337 DOI: 10.1038/S41557-020-0423-6 |
0.33 |
|
| 2020 |
Sharma G, Jayasinghe-Arachchige VM, Hu Q, Schenk G, Prabhakar R. Effect of chemically distinct substrates on the mechanism and reactivity of a highly promiscuous metallohydrolase Acs Catalysis. 10: 3684-3696. DOI: 10.1021/Acscatal.9B04847 |
0.416 |
|
| 2020 |
Hu Q, Jayasinghe‐Arachchige VM, Sharma G, Serafim LF, Paul TJ, Prabhakar R. Mechanisms of peptide and phosphoester hydrolysis catalyzed by two promiscuous metalloenzymes (insulin degrading enzyme and glycerophosphodiesterase) and their synthetic analogues Wiley Interdisciplinary Reviews: Computational Molecular Science. 10. DOI: 10.1002/Wcms.1466 |
0.432 |
|
| 2019 |
Hu Q, Jayasinghe-Arachchige VM, Zuchniarz J, Prabhakar R. Effects of the Metal Ion on the Mechanism of Phosphodiester Hydrolysis Catalyzed by Metal-Cyclen Complexes. Frontiers in Chemistry. 7: 195. PMID 31024887 DOI: 10.3389/Fchem.2019.00195 |
0.344 |
|
| 2019 |
Duay SS, Sharma G, Prabhakar R, Angeles-Boza AM, May ER. Molecular Dynamics Investigation into the Effect of Zinc(II) on the Structure and Membrane Interactions of the Antimicrobial Peptide Clavanin A. The Journal of Physical Chemistry. B. PMID 30908921 DOI: 10.1021/Acs.Jpcb.8B11496 |
0.367 |
|
| 2019 |
Sharma G, Hu Q, Jayasinghe-Arachchige VM, Paul TJ, Schenk G, Prabhakar R. Investigating coordination flexibility of glycerophosphodiesterase (GpdQ) through interactions with mono-, di-, and triphosphoester (NPP, BNPP, GPE, and paraoxon) substrates. Physical Chemistry Chemical Physics : Pccp. PMID 30785142 DOI: 10.1039/C8Cp07031H |
0.417 |
|
| 2018 |
Jayasinghe-Arachchige VM, Hu Q, Sharma G, Paul TJ, Lundberg M, Quinonero D, Parac-Vogt TN, Prabhakar R. Hydrolysis of chemically distinct sites of human serum albumin by polyoxometalate: A hybrid QM/MM (ONIOM) study. Journal of Computational Chemistry. PMID 30238478 DOI: 10.1002/Jcc.25528 |
0.4 |
|
| 2018 |
Paul TJ, Parac-Vogt T, Quiñonero D, Prabhakar R. Investigating Polyoxometalate-Protein Interactions at Chemically Distinct Binding Sites. The Journal of Physical Chemistry. B. PMID 29975530 DOI: 10.1021/Acs.Jpcb.8B02931 |
0.363 |
|
| 2018 |
Paul TJ, Schenk G, Prabhakar R. Formation of Catalytically Active Binuclear Center of Glycerophosphodiesterase (GpdQ): A Molecular Dynamics Study. The Journal of Physical Chemistry. B. PMID 29723477 DOI: 10.1021/Acs.Jpcb.8B02046 |
0.421 |
|
| 2017 |
Zhang T, Sharma G, Paul TJ, Hoffmann Z, Prabhakar R. Effects of Ligand Environment in Zr(IV) Assisted Peptide Hydrolysis. Journal of Chemical Information and Modeling. PMID 28398040 DOI: 10.1021/Acs.Jcim.6B00781 |
0.39 |
|
| 2017 |
Lee HJ, Korshavn KJ, Nam Y, Kang J, Paul TJ, Kerr RA, Youn IS, Ozbil M, Kim KS, Ruotolo BT, Prabhakar R, Ramamoorthy A, Lim MH. Structural and Mechanistic Insights into Development of Chemical Tools to Control Individual and Inter-Related Pathological Features in Alzheimer's Disease. Chemistry (Weinheim An Der Bergstrasse, Germany). 23: 2706-2715. PMID 28004889 DOI: 10.1002/Chem.201605401 |
0.74 |
|
| 2017 |
Aliyan A, Paul TJ, Jiang B, Pennington C, Sharma G, Prabhakar R, Martí AA. Photochemical Identification of Molecular Binding Sites on the Surface of Amyloid-β Fibrillar Aggregates Chem. 3: 898-912. DOI: 10.1016/J.Chempr.2017.09.011 |
0.39 |
|
| 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 |
0.799 |
|
| 2016 |
Paul TJ, Hoffmann Z, Wang C, Shanmugasundaram M, de Joannis J, Shekhtman A, Lednev IK, Yadavalli VK, Prabhakar R. Structural and Mechanical Properties of Amyloid beta Fibrils: A Combined Experimental and Theoretical Approach. The Journal of Physical Chemistry Letters. PMID 27387853 DOI: 10.1021/Acs.Jpclett.6B01066 |
0.359 |
|
| 2016 |
Paul TJ, Kelly H, Zuchniarz J, Ahmed T, Prabhakar R. Design of heparin oligosaccharide based molecules for inhibition of Alzheimer amyloid beta (Aβ40) aggregation Canadian Journal of Chemistry. 94: 1090-1098. DOI: 10.1139/Cjc-2016-0292 |
0.373 |
|
| 2015 |
Derrick JS, Kerr RA, Nam Y, Oh SB, Lee HJ, Earnest KG, Suh N, Peck KL, Ozbil M, Korshavn KJ, Ramamoorthy A, Prabhakar R, Merino EJ, Shearer J, Lee JY, et al. A Redox-Active, Compact Molecule for Cross-Linking Amyloidogenic Peptides into Nontoxic, Off-Pathway Aggregates: In Vitro and In Vivo Efficacy and Molecular Mechanisms. Journal of the American Chemical Society. 137: 14785-97. PMID 26575890 DOI: 10.1021/Jacs.5B10043 |
0.761 |
|
| 2015 |
Song ES, Ozbil M, Zhang T, Sheetz M, Lee D, Tran D, Li S, Prabhakar R, Hersh LB, Rodgers DW. An Extended Polyanion Activation Surface in Insulin Degrading Enzyme. Plos One. 10: e0133114. PMID 26186535 DOI: 10.1371/Journal.Pone.0133114 |
0.752 |
|
| 2015 |
Libardo MD, Paul TJ, Prabhakar R, Angeles-Boza AM. Hybrid peptide ATCUN-sh-Buforin: Influence of the ATCUN charge and stereochemistry on antimicrobial activity. Biochimie. 113: 143-55. PMID 25891844 DOI: 10.1016/J.Biochi.2015.04.008 |
0.384 |
|
| 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 |
0.797 |
|
| 2015 |
Song ES, Ozbil M, Zhang T, Sheetz M, Lee D, Tran D, Li S, Prabhakar R, Hersh LB, Rodgers DW. An extended polyanion activation surface in insulin degrading enzyme Plos One. 10. DOI: 10.1371/journal.pone.0133114 |
0.692 |
|
| 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 |
0.775 |
|
| 2014 |
Zhang T, Zhu X, Prabhakar R. Mechanistic insights into metal (Pd2+, Co2+, and Zn2+)-β-cyclodextrin catalyzed peptide hydrolysis: a QM/MM approach. The Journal of Physical Chemistry. B. 118: 4106-14. PMID 24713044 DOI: 10.1021/Jp502229S |
0.371 |
|
| 2013 |
Elton ES, Zhang T, Prabhakar R, Arif AM, Berreau LM. Pb(II)-promoted amide cleavage: mechanistic comparison to a Zn(II) analogue. Inorganic Chemistry. 52: 11480-92. PMID 24066688 DOI: 10.1021/Ic401782X |
0.314 |
|
| 2013 |
Cook NP, Ozbil M, Katsampes C, Prabhakar R, Martí AA. Unraveling the photoluminescence response of light-switching ruthenium(II) complexes bound to amyloid-β. Journal of the American Chemical Society. 135: 10810-6. PMID 23845146 DOI: 10.1021/Ja404850U |
0.744 |
|
| 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 |
0.783 |
|
| 2013 |
Liu Y, Mukherjee A, Nahumi N, Ozbil M, Brown D, Angeles-Boza AM, Dooley DM, Prabhakar R, Roth JP. Experimental and computational evidence of metal-O2 activation and rate-limiting proton-coupled electron transfer in a copper amine oxidase. The Journal of Physical Chemistry. B. 117: 218-29. PMID 23240607 DOI: 10.1021/Jp3121484 |
0.725 |
|
| 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 |
0.706 |
|
| 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 |
0.794 |
|
| 2012 |
Kurouski D, Washington J, Ozbil M, Prabhakar R, Shekhtman A, Lednev IK. Disulfide bridges remain intact while native insulin converts into amyloid fibrils. Plos One. 7: e36989. PMID 22675475 DOI: 10.1371/Journal.Pone.0036989 |
0.731 |
|
| 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 |
0.731 |
|
| 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 |
0.762 |
|
| 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 |
0.789 |
|
| 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 |
0.733 |
|
| 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 |
0.786 |
|
| 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 |
0.718 |
|
| 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 |
0.769 |
|
| 2010 |
Bora RP, Prabhakar R. Elucidation of interactions of Alzheimer amyloid beta peptides (Abeta40 and Abeta42) with insulin degrading enzyme: a molecular dynamics study. Biochemistry. 49: 3947-56. PMID 20380468 DOI: 10.1021/Bi1002103 |
0.485 |
|
| 2010 |
Bora RP, Ozbil M, Prabhakar R. Elucidation of insulin degrading enzyme catalyzed site specific hydrolytic cleavage of amyloid beta peptide: a comparative density functional theory study. Journal of Biological Inorganic Chemistry : Jbic : a Publication of the Society of Biological Inorganic Chemistry. 15: 485-95. PMID 20033747 DOI: 10.1007/S00775-009-0617-2 |
0.788 |
|
| 2010 |
Kumar A, Zhu X, Walsh K, Prabhakar R. Theoretical insights into the mechanism of selective Peptide bond hydrolysis catalyzed by [Pd(H(2)O)(4)](2+). Inorganic Chemistry. 49: 38-46. PMID 19958017 DOI: 10.1021/Ic901071V |
0.415 |
|
| 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 |
0.685 |
|
| 2009 |
Prabhakar R. Computational insights into the development of novel therapeutic strategies for Alzheimer's disease. Future Medicinal Chemistry. 1: 119-35. PMID 21426072 DOI: 10.4155/Fmc.09.10 |
0.341 |
|
| 2009 |
Bora RP, Prabhakar R. Translational, rotational and internal dynamics of amyloid beta-peptides (Abeta40 and Abeta42) from molecular dynamics simulations. The Journal of Chemical Physics. 131: 155103. PMID 20568886 DOI: 10.1063/1.3249609 |
0.354 |
|
| 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 |
0.768 |
|
| 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 |
0.753 |
|
| 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 |
0.685 |
|
| 2008 |
Triguero L, Singh R, Prabhakar R. Comparative molecular dynamics studies of wild-type and oxidized forms of full-length Alzheimer amyloid beta-peptides Abeta(1-40) and Abeta(1-42). The Journal of Physical Chemistry. B. 112: 7123-31. PMID 18476733 DOI: 10.1021/Jp801168V |
0.41 |
|
| 2008 |
Triguero L, Singh R, Prabhakar R. Molecular dynamics study to investigate the effect of chemical substitutions of methionine 35 on the secondary structure of the amyloid beta (Abeta(1-42)) monomer in aqueous solution. The Journal of Physical Chemistry. B. 112: 2159-67. PMID 18220385 DOI: 10.1021/Jp0771872 |
0.382 |
|
| 2006 |
Prabhakar R, Vreven T, Frisch MJ, Morokuma K, Musaev DG. Is the protein surrounding the active site critical for hydrogen peroxide reduction by selenoprotein glutathione peroxidase? An ONIOM study. The Journal of Physical Chemistry. B. 110: 13608-13. PMID 16821888 DOI: 10.1021/Jp0619181 |
0.418 |
|
| 2006 |
Prabhakar R, Morokuma K, Hill CL, Musaev DG. Insights into the mechanism of selective olefin epoxidation catalyzed by [gamma-(SiO4)W10O32H4]4-. A computational study. Inorganic Chemistry. 45: 5703-9. PMID 16813436 DOI: 10.1021/Ic060725P |
0.361 |
|
| 2006 |
Prabhakar R, Morokuma K, Musaev DG. A DFT study of the mechanism of Ni superoxide dismutase (NiSOD): role of the active site cysteine-6 residue in the oxidative half-reaction. Journal of Computational Chemistry. 27: 1438-45. PMID 16804959 DOI: 10.1002/Jcc.20455 |
0.387 |
|
| 2006 |
Prabhakar R, Morokuma K, Musaev DG. Peroxynitrite reductase activity of selenoprotein glutathione peroxidase: a computational study. Biochemistry. 45: 6967-77. PMID 16734432 DOI: 10.1021/Bi060456E |
0.339 |
|
| 2005 |
Prabhakar R, Vreven T, Morokuma K, Musaev DG. Elucidation of the mechanism of selenoprotein glutathione peroxidase (GPx)-catalyzed hydrogen peroxide reduction by two glutathione molecules: a density functional study. Biochemistry. 44: 11864-71. PMID 16128588 DOI: 10.1021/Bi050815Q |
0.355 |
|
| 2005 |
Prabhakar R, Morokuma K, Musaev DG. A comparative study of various computational approaches in calculating the structure of pyridoxal 5'-phosphate (PLP)-dependent beta-lyase protein. The importance of protein environment. Journal of Computational Chemistry. 26: 443-6. PMID 15688436 DOI: 10.1002/Jcc.20179 |
0.348 |
|
| 2004 |
Prabhakar R, Siegbahn PEM. A Theoretical Study of the Mechanism for the Biogenesis of Cofactor Topaquinone in Copper Amine Oxidases Journal of the American Chemical Society. 126: 3996-4006. PMID 15038754 DOI: 10.1021/Ja034721K |
0.516 |
|
| 2004 |
Prabhakar R, Siegbahn PEM, Minaev BF, Ågren H. Spin transition during H2O2 formation in the oxidative half-reaction of copper amine oxidases Journal of Physical Chemistry B. 108: 13882-13892. DOI: 10.1021/Jp0478312 |
0.462 |
|
| 2004 |
Prabhakar R, Musaev DG, Khavrutskii IV, Morokuma K. Does the active site of mammalian glutathione peroxidase (GPx) contain water molecules? An ONIOM study Journal of Physical Chemistry B. 108: 12643-12645. DOI: 10.1021/Jp047303Q |
0.321 |
|
| 2003 |
Prabhakar R, Siegbahn PEM. A comparison of the mechanism for the reductive half-reaction between pea seedling and other copper amine oxidases (CAOs) Journal of Computational Chemistry. 24: 1599-1609. PMID 12926004 DOI: 10.1002/Jcc.10282 |
0.556 |
|
| 2003 |
Prabhakar R, Siegbahn PEM, Minaev BF. A theoretical study of the dioxygen activation by glucose oxidase and copper amine oxidase Biochimica Et Biophysica Acta - Proteins and Proteomics. 1647: 173-178. PMID 12686129 DOI: 10.1016/S1570-9639(03)00090-6 |
0.492 |
|
| 2003 |
Prabhakar R, Siegbahn PEM. Theoretical Study of the Mechanism for the Oxidative Half-Reaction of Copper Amine Oxidase (CAO) Journal of Physical Chemistry B. 107: 3944-3953. DOI: 10.1021/Jp0272062 |
0.522 |
|
| 2002 |
Prabhakar R, Siegbahn PEM, Minaev BF, Ågren H. Activation of triplet dioxygen by glucose oxidase: Spin-orbit coupling in the superoxide ion Journal of Physical Chemistry B. 106: 3742-3750. DOI: 10.1021/Jp014013Q |
0.457 |
|
| 2001 |
Prabhakar R, Siegbahn PEM. A theoretical study of the mechanism for the reductive half-reaction of pea seedling amine oxidase (PSAO) Journal of Physical Chemistry B. 105: 4400-4408. DOI: 10.1021/Jp003343S |
0.524 |
|
| 2000 |
Prabhakar R, Blomberg MRA, Siegbahn PEM. A density functional theory study of a concerted mechanism for proton exchange between amino acid side chains and water Theoretical Chemistry Accounts. 104: 461-470. DOI: 10.1007/S002140000170 |
0.47 |
|
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