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Abir Ganguly
Abir Ganguly
Director & Head of Free Energy, TandemAI
Verified email at tandemai.com - Homepage
Title
Cited by
Cited by
Year
Quantum mechanical/molecular mechanical free energy simulations of the self-cleavage reaction in the hepatitis delta virus ribozyme
A Ganguly, P Thaplyal, E Rosta, PC Bevilacqua, S Hammes-Schiffer
Journal of the American Chemical Society 136 (4), 1483-1496, 2014
742014
Role of the Active Site Guanine in the glmS Ribozyme Self-Cleavage Mechanism: Quantum Mechanical/Molecular Mechanical Free Energy Simulations
S Zhang, A Ganguly, P Goyal, JL Bingaman, PC Bevilacqua, ...
Journal of the American Chemical Society 137 (2), 784-798, 2015
632015
Thio effects and an unconventional metal ion rescue in the genomic hepatitis delta virus ribozyme
P Thaplyal, A Ganguly, BL Golden, S Hammes-Schiffer, PC Bevilacqua
Biochemistry 52 (37), 6499-6514, 2013
592013
Inverse thio effects in the hepatitis delta virus ribozyme reveal that the reaction pathway is controlled by metal ion charge density
P Thaplyal, A Ganguly, S Hammes-Schiffer, PC Bevilacqua
Biochemistry 54 (12), 2160-2175, 2015
582015
Changes in active site histidine hydrogen bonding trigger cryptochrome activation
A Ganguly, CC Manahan, D Top, EF Yee, C Lin, MW Young, W Thiel, ...
Proceedings of the National Academy of Sciences 113 (36), 10073-10078, 2016
552016
Metal binding motif in the active site of the HDV ribozyme binds divalent and monovalent ions
N Veeraraghavan, A Ganguly, JH Chen, PC Bevilacqua, ...
Biochemistry 50 (13), 2672-2682, 2011
542011
An ontology for facilitating discussion of catalytic strategies of RNA-cleaving enzymes
PC Bevilacqua, ME Harris, JA Piccirilli, C Gaines, A Ganguly, ...
ACS chemical biology 14 (6), 1068-1076, 2019
502019
Importance of MM polarization in QM/MM studies of enzymatic reactions: assessment of the QM/MM Drude oscillator model
A Ganguly, E Boulanger, W Thiel
Journal of Chemical Theory and Computation 13 (6), 2954-2961, 2017
442017
Identification of the Catalytic Mg2+ Ion in the Hepatitis Delta Virus Ribozyme
J Chen, A Ganguly, Z Miswan, S Hammes-Schiffer, PC Bevilacqua, ...
Biochemistry 52 (3), 557-567, 2013
442013
Transport properties of tetrahedral, network-forming ionic melts
M Agarwal, A Ganguly, C Chakravarty
The Journal of Physical Chemistry B 113 (46), 15284-15292, 2009
412009
Mechanistic strategies in the HDV ribozyme: chelated and diffuse metal ion interactions and active site protonation
N Veeraraghavan, A Ganguly, BL Golden, PC Bevilacqua, ...
The Journal of Physical Chemistry B 115 (25), 8346-8357, 2011
392011
Confluence of theory and experiment reveals the catalytic mechanism of the Varkud satellite ribozyme
A Ganguly, BP Weissman, TJ Giese, NS Li, S Hoshika, S Rao, SA Benner, ...
Nature chemistry 12 (2), 193-201, 2020
322020
Tuning flavin environment to detect and control light-induced conformational switching in Drosophila cryptochrome
S Chandrasekaran, CM Schneps, R Dunleavy, C Lin, CC DeOliveira, ...
Communications biology 4 (1), 249, 2021
282021
Glutamine amide flip elicits long distance allosteric responses in the LOV protein Vivid
A Ganguly, W Thiel, BR Crane
Journal of the American Chemical Society 139 (8), 2972-2980, 2017
282017
Evidence for a catalytic strategy to promote nucleophile activation in metal-dependent RNA-cleaving ribozymes and 8-17 DNAzyme
A Ganguly, BP Weissman, JA Piccirilli, DM York
ACS catalysis 9 (12), 10612-10617, 2019
252019
Excess entropy and structural transitions in a two-dimensional square-shoulder fluid
M Singh, H Liu, SK Kumar, A Ganguly, C Chakravarty
The Journal of chemical physics 132 (7), 2010
242010
Quantum mechanical/molecular mechanical study of the HDV ribozyme: impact of the catalytic metal ion on the mechanism
A Ganguly, PC Bevilacqua, S Hammes-Schiffer
The journal of physical chemistry letters 2 (22), 2906-2911, 2011
222011
Elucidation of the catalytic mechanism of a miniature zinc finger hydrolase
A Ganguly, TQ Luong, O Brylski, M Dirkmann, D Möller, S Ebbinghaus, ...
The Journal of Physical Chemistry B 121 (26), 6390-6398, 2017
212017
Mechanistic insight into light-dependent recognition of Timeless by Drosophila Cryptochrome
C Lin, CM Schneps, S Chandrasekaran, A Ganguly, BR Crane
Structure 30 (6), 851-861. e5, 2022
132022
AMBER free energy tools: a new framework for the design of optimized alchemical transformation pathways
HC Tsai, TS Lee, A Ganguly, TJ Giese, MC Ebert, P Labute, KM Merz Jr, ...
Journal of Chemical Theory and Computation 19 (2), 640-658, 2023
112023
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