| 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 | 75 | 2014 |
| 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 | 73 | 2020 |
| 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 | 64 | 2015 |
| 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 | 63 | 2013 |
| 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 | 59 | 2015 |
| 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 | 56 | 2016 |
| 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 | 55 | 2011 |
| 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 | 52 | 2019 |
| 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 | 48 | 2013 |
| 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 | 44 | 2017 |
| 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 | 41 | 2009 |
| 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 | 40 | 2011 |
| 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 | 28 | 2021 |
| 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 | 28 | 2017 |
| 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 | 25 | 2019 |
| 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 | 24 | 2010 |
| 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 | 23 | 2011 |
| 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 | 21 | 2017 |
| 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 | 15 | 2023 |
| ACES: optimized alchemically enhanced sampling TS Lee, HC Tsai, A Ganguly, DM York Journal of Chemical Theory and Computation 19 (2), 472-487, 2023 | 14 | 2023 |
Philip BevilacquaProfessor of Chemistry, The Pennsylvania State UniversityVerified email at psu.edu
