Abir Ganguly

Abdelmalek Essaâdi University — MA

Biochemistry, Genetics and Molecular Biology · Life Sciences

20h-index995citations33works3.02yr avg
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Research Topics

Protein Structure and Dynamics(13), RNA and protein synthesis mechanisms(11), Computational Drug Discovery Methods(7), Light effects on plants(7), Photoreceptor and optogenetics research(7)

Publications33 total

A Relative Binding Free Energy Framework for Structurally Dissimilar Molecules
Journal of Chemical Information and Modeling·2026
Improvements in Precision of Relative Binding Free Energy Calculations Afforded by the Alchemical Enhanced Sampling (ACES) Approach
Journal of Chemical Information and Modeling·2024· 6 citedOpen Access
ACES: Optimized Alchemically Enhanced Sampling
Journal of Chemical Theory and Computation·2023· 50 citedOpen Access
AMBER Free Energy Tools: A New Framework for the Design of Optimized Alchemical Transformation Pathways
Journal of Chemical Theory and Computation·2023· 38 citedOpen Access
AMBER Drug Discovery Boost Tools: Automated Workflow for Production Free-Energy Simulation Setup and Analysis (ProFESSA)
Journal of Chemical Information and Modeling·2022· 33 citedOpen Access
Room-temperature serial synchrotron crystallography of <i>Drosophila</i> cryptochrome
Acta Crystallographica Section D Structural Biology·2022· 9 citedOpen Access
Introducing a New Bond-Forming Activity in an Archaeal DNA Polymerase by Structure-Guided Enzyme Redesign
ACS Chemical Biology·2022· 4 citedOpen Access
Mechanistic insight into light-dependent recognition of Timeless by Drosophila Cryptochrome
Structure·2022· 24 citedOpen Access
Introducing a New Bond-Forming Activity in an Archaeal DNA Polymerase by Structure-Guided Enzyme Redesign
2021· 1 citedOpen Access
Robust, Efficient and Automated Methods for Accurate Prediction of Protein-Ligand Binding Affinities in AMBER Drug Discovery Boost
ACS symposium series·2021· 18 cited
Mechanistic insight into light-dependent recognition of Timeless by Drosophila cryptochrome
2021· 1 citedOpen Access
Robust, Efficient and Automated Methods for Accurate Prediction of Protein-Ligand Binding Affinities in AMBER Drug Discovery Boost
2021Open Access
Robust, Efficient and Automated Methods for Accurate Prediction of Protein-Ligand Binding Affinities in AMBER Drug Discovery Boost
2021Open Access
Peripheral Methionine Residues Impact Flavin Photoreduction and Protonation in an Engineered LOV Domain Light Sensor
Biochemistry·2021· 10 citedOpen Access
Tuning flavin environment to detect and control light-induced conformational switching in Drosophila cryptochrome
Communications Biology·2021· 47 citedOpen Access
Confluence of theory and experiment reveals the catalytic mechanism of the Varkud satellite ribozyme
Nature Chemistry·2020· 54 citedOpen Access
Evidence for a Catalytic Strategy to Promote Nucleophile Activation in Metal-Dependent RNA-Cleaving Ribozymes and 8-17 DNAzyme
ACS Catalysis·2019· 30 citedOpen Access
An Ontology for Facilitating Discussion of Catalytic Strategies of RNA-Cleaving Enzymes
ACS Chemical Biology·2019· 58 citedOpen Access
Elucidation of the Catalytic Mechanism of a Miniature Zinc Finger Hydrolase
The Journal of Physical Chemistry B·2017· 23 cited
Importance of MM Polarization in QM/MM Studies of Enzymatic Reactions: Assessment of the QM/MM Drude Oscillator Model
Journal of Chemical Theory and Computation·2017· 49 cited
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Frequent Co-authors

Darrin M. York(14), Philip C. Bevilacqua(9), Sharon Hammes‐Schiffer(8), Timothy J. Giese(8), Tai‐Sung Lee(8), Brian R. Crane(7), Hsu‐Chun Tsai(7), Changfan Lin(4), Walter Thiel(4), Barbara L. Golden(4), Connor M. Schneps(4), Pallavi Thaplyal(3), Joseph A. Piccirilli(3), Siddarth Chandrasekaran(3), Estella F. Yee(2), Benjamin P. Weissman(2), Narayanan Veeraraghavan(2), Charusita Chakravarty(2), James Xu(2), Yinhui Yi(2)