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Publications
] , “Conformational properties of amphotericin B amide derivatives--impact on selective toxicity.”, J Comput Aided Mol Des, vol. 14, no. 7, pp. 689-703, 2000.
, “Modeling the deamidation of asparagine residues via succinimide intermediates”, vol. 7, no. 5, pp. 147 - 160, 2001.
, “Modelling the hydrolysis of succinimide: formation of aspartate and reversible isomerization of aspartic acid via succinimide.”, Org Biomol Chem, vol. 1, no. 13, pp. 2290-7, 2003.
, “Barriers to internal rotation around the C-N bond in 3-(o-aryl)-5-methyl-rhodanines using NMR spectroscopy and computational studies. Electron density topological analysis of the transition states.”, Org Biomol Chem, vol. 2, no. 17, pp. 2426-36, 2004.
, “Theoretical Approach to the Wear and Tear Mechanism in Triosephoshate Isomerase: A QM/MM Study”, The Journal of Physical Chemistry B, vol. 108, pp. 3925-3934, 2004.
, “Coupling of structural fluctuations to deamidation reaction in triosephosphate isomerase by Gaussian network model.”, Proteins, vol. 62, no. 3, pp. 715-27, 2006.
, “Mechanistic Study on [3+2] Cycloaddition and Cyclopropanation Reactions of 1,3-Dioxepine Derivatives in the Presence of Copper(I) Catalyst”, Organometallics, vol. 28, pp. 4964-4973, 2009.
, “A computational study on the mechanism and the kinetics of urethane formation”, Computational and Theoretical Chemistry, vol. 963, pp. 168-175, 2011.
, “Theoretical studies on the inactivation mechanism of γ-aminobutyric acid aminotransferase.”, Org Biomol Chem, vol. 9, no. 14, pp. 5162-71, 2011.
, “Solvent-catalyzed ring-chain-ring tautomerization in axially chiral compounds.”, Chemistry, vol. 18, no. 40, pp. 12725-32, 2012.
, “Theoretical study on HF elimination and aromatization mechanisms: a case of pyridoxal 5' phosphate-dependent enzyme.”, J Org Chem, vol. 77, no. 13, pp. 5533-43, 2012.
, “Stereoelectronic explanations for the mechanistic details of transimination and HF elimination reactions.”, J Mol Graph Model, vol. 51, pp. 173-83, 2014.
, “A Theoretical Study On Rh(I) Catalyzed Enantioselective Conjugate Addition Reactions of Fluoroalkylated Olefins”, Organometallics, vol. 33, pp. 5111-5119, 2014.
, “Role of the n+1 amino acid residue on the deamidation of asparagine in pentapeptides”, Molecular Physics, vol. 113, pp. 3839–3848, 2015.
, “Molecular dynamics simulations of apo, holo, and inactivator bound GABA-at reveal the role of active site residues in PLP dependent enzymes.”, Proteins, vol. 84, no. 7, pp. 875-91, 2016.
, “Bismuth nitrate-promoted disproportionative condensation of indoles with cyclohexanone: a new-type azafulvenium reactivity of indole”, New J. Chem., vol. 41, pp. 9674-9687, 2017.
, “A computational insight into cyclopropenone activated dehydration reaction of alcohols.”, J Mol Graph Model, vol. 77, pp. 106-114, 2017.
, “Monte Carlo and Molecular Dynamics Simulations suggest controlled release of corticosteroids from mesoporous host MIL-101 (Cr)”, Molecular Simulation, vol. 47, pp. 1530–1539, 2021.
, “Repurposing of FDA-approved drugs against active site and potential allosteric drug-binding sites of COVID-19 main protease”, Proteins: Structure, Function, and Bioinformatics, vol. 89, pp. 1425-1441, 2021.
, “Molecular Mechanism of Protein Arginine Deiminase 2: A Study Involving Multiple Microsecond Long Molecular Dynamics Simulations”, Biochemistry, vol. 61, pp. 1286-1297, 2022.
, “Mechanistic insights into the challenges of organocatalytic Beckmann rearrangement reactions”, Org. Biomol. Chem., vol. 21, pp. 1254-1263, 2023.
, “A computational workflow to determine drug candidates alternative to aminoglycosides targeting the decoding center of E. coli ribosome”, Journal of Molecular Graphics and Modelling, vol. 131, p. 108817, 2024.
, “Innovative Use of an Injectable, Self-Healing Drug-Loaded Pectin-Based Hydrogel for Micro- and Supermicro-Vascular Anastomoses”, Biomacromolecules, vol. 25, pp. 3959-3975, 2024.
, “Computational insights into substrate-assisted citrullination mechanisms of PAD2 isozyme: A comparative analysis of reaction pathways”, Journal of Molecular Graphics and Modelling, vol. 140, p. 109107, 2025.
, “Graphene oxide-based and porous nanocarriers for drug delivery developed with computational and experimental approaches”, Surfaces and Interfaces, vol. 76, p. 107860, 2025.
, “In Silico Identification of Putative Allosteric Pockets and Inhibitors for the KRASG13D-SOS1 Complex in Cancer Therapy”, International Journal of Molecular Sciences, vol. 26, p. 3293, 2025.
, “Multiscale Modeling of the Bacterial Ribosome to Identify Potential Peptide Modulators and Their Allosteric Effects”, BiochemistryBiochemistry, 2026.
, “A multi-stage computational pipeline and in vitro validation for the discovery of small-molecule translation inhibitors targeting the bacterial ribosome”, RSC Advances, vol. 16, no. 20, pp. 18359 - 18373, 2026.
, “RinPy, a Python Package for Residue Interaction Network Model to Analyze Protein Structures and Predict Ligand Binding Sites”, Journal of Chemical Information and ModelingJournal of Chemical Information and Modeling, 2026.
, “Synthesis, biological evaluation and molecular docking of novel 2-pyrazoline-1-carboxamides as anti-Alzheimer agents”, Future Medicinal ChemistryFuture Medicinal Chemistry, vol. 18, no. 1, pp. 1 - 17, 2026.
, “Synthesis, Molecular Docking, Molecular Dynamics and DFT Studies of New Thiazole Derivatives as Dual Cholinesterase Inhibitors Against Alzheimer’s Disease”, Polycyclic Aromatic Compounds, pp. 1–25, 2026.