A new reaction coordinate to study the translocation pathway of cell-penetrating peptides across lipid bilayers: The cases of transportan-10 and penetratin.
A. V. Mathath and D. Chakraborty*, J. Chem. Phys., 163, 244104 (2025).
pH-dependent peptide aggregation and translocation across octanol and hexane interfaces: insights from umbrella sampling simulations. A. V. Mathath, S. Sarkar and D. Chakraborty*, Phys. Chem. Chem. Phys., DOI: 10.1039/D5CP03690A (2026).
The 4E-BPs as Translational Regulators in Neurological Disorders: Molecular Mechanisms and Therapeutic Potential. S. S Baskarapantula, V. S. Kumar, P. Changdar, D. Chakraborty, Y. Nayak, A. R. L. Spada, C. L. Bennett, S. G. Dastidar, Mol. Neurobiol., 63, 165 (2026).
Controlling the Morphology and Orientation of the Helical Self‐Assembly of Pyrazine Derivatives by Tuning Hydration Shells. S. Sarkar, A. V. Mathath and D. Chakraborty*, ChemPhysChem, e202400951 (2025). https://doi.org/10.1002/cphc.202400951
Effect of peptide hydrophilicity on membrane curvature and permeation. A. V. Mathath and D. Chakraborty*, J. Chem. Phys., 161, 164105 (2024).
Evaluating the Impact of the Membrane Thickness on the Function of the Intramembrane Protease GlpG.
O Engberg, AV Mathath, V Döbel, C Frie, MK Lemberg, D. Chakraborty, D. Huster*, Biophys. J. (accepted) (2024). DOI: https://doi.org/10.1016/j.bpj.2024.10.019.
Study of Correlated Motions to Detect the Conformational Transitions of Intrinsically Disordered Sheep Prion Peptide. D. Chakraborty*, O. Singh and D. Parameswaran, J. Chem. Inf. Model., 64, 5590 (2024).
Designing Reaction Coordinate for Ion-Induced Pore-Assisted Mechanism of Halide Ions Permeation through Lipid Bilayer by Umbrella Sampling. A. V. Mathath, B. K. Das, D. Chakraborty*, J. Chem. Inf. Model., 63, 7778–7790 (2023).
Exploring the barriers in the aggregation of hexadecameric human prion peptide through Markov state model. B. K. Das, O. Singh and D. Chakraborty*, ACS Chemical Neuroscience., 14, 3622-3645 (2023).
Vetting of New 2,5-Bis (2,2,2-trifluoroethoxy) Phenyl-Linked 1,3-Thiazolidine-4-one Derivatives as AURKA and VEGFR-2 Inhibitor Antiglioma Agents Assisted with In Vitro and In Silico Studies. S. D. Shankara, A. M Isloor, P. K Jayaswamy, P. Shetty, D. Chakraborty, P. P. Venugopal, ACS omega, 8, 43596–43609 (2023).
Effect of Water Models on The Stability of RNA: Role of Counter-Ions. O. Singh, P. Venugopal, D. Chakraborty*, Chemical Physics Impact, 7, 100313 (2023).
Growth Reaction of Gold Nanorod in Presence of Mutated Peptides and Amine Modified Single Strand Nucleic Acid. JK Sahu, O Singh, D Chakraborty*, KK Sadhu*, Chem. Asian. J., 18, 8, e202300049 (2023).
A chemically robust amine-grafted Zn (ii)-based smart supramolecular gel as a regenerative platform for trace discrimination of nitro-antibiotics and assorted environmental toxins. E Saha, A Chhetri, PP Venugopal, D Chakraborty*, J Mitra*, J. Mater Chem. C, 11, 3252 (2023).
Understanding the role of Water on Temperature-dependent Structural Modifications of SARS CoV-2 Main Protease Binding Sites. P. P. Venugopal, O. Singh and D. Chakraborty*, J. Mol. Liq, 363, 119867 (2022).
Exploring the multiple conformational states of RNA genome through interhelical dynamics and network analysis. O. Singh, P. P. Venugopal, A. Mathur and D. Chakraborty*, J. Mol. Graph. Model., 116, 108264 (2022).
Influence of ion specificity and concentration on the conformational transition of intrinsically disordered sheep prion peptide. O. Singh, B. K. Das, D. Chakraborty*, Chem. Phys. Chem, 23, e202200211 (2022).
2,5-Bis(2,2,2-trifluoroethoxy)phenyl-tethered 1,3,4-Oxadiazoles Derivatives: Synthesis, In Silico Studies, and Biological Assessment as Potential Candidates for Anti-Cancer and Anti- Diabetic Agent. S. D. Shankara, A. M. Isloor *, A. K. Kudva, S. V, Raghu, P. K. Jayaswamy, P. P. Venugopal, P. Shetty, D. Chakraborty, Molecules, 27, 8694 (2022).
Anti-corrosion investigation of a new Nitro Veratraldehyde substituted Imidazopyridine derivative Schiff base on Mild Steel surface in Hydrochloric acid medium: Experimental, Computational, Surface morphological analysis. V. K. Shenoy, P. P. Venugopal, Reena Kumari P. D.*; D. Chakraborty*, Mater. Chem. Phys., 281, 125855 (2022).
Temperature-dependent Conformational Evolution of SARS CoV-2 RNA Genome Using Network Analysis. Omkar Singh, Pushyaraga P Venugopal, Apoorva Mathur and D. Chakraborty*, J. Phys. Chem. B, 125, 10672 (2021).
Preferential binding affinity of ions and their effect on structure and dynamics of water near antimicrobial peptide Omkar Singh and D. Chakraborty*, J. Mol. Liq., 344, 117789 (2021).
Exploring the potential role of quercetin in corrosion inhibition of aluminium alloy 6063 in hydrochloric acid solution by experimental and theoretical studies D. Kumari, Pushyaraga P Venugopal; Reena Kumari P D*; D. Chakraborty* J Adhes Sci Technol, 36, 2020-2045 (2021).
Deciphering the Competitive Inhibition of Dihydropteroate Synthase by 8 Marcaptoguanine Analogues: Enhanced Potency in Phenylsulfonyl fragments B. K. Das and D. Chakraborty*, J. Biomol. Struct. Dyn. , 40, 13083-13102 (2022).
Theoretical Insights into Molecular Mechanism and Energy Criteria of PARP‐2 Enzyme Inhibition by Benzimidazole Analogues. Pushyaraga P Venugopal, M Shilpa and D. Chakraborty*, Proteins, 89, 988 (2021).
Epitope-Based Potential Vaccine Candidate for Humoral and Cell-Mediated Immunity to Combat Severe Acute Respiratory Syndrome Coronavirus 2 Pandemic. B. K. Das and D. Chakraborty*, J. Phys. Chem. Lett., 11, 9920 (2020).
Molecular mechanism of inhibition of COVID-19 main protease by β-adrenoceptor agonists and adenosine deaminase inhibitors using in silico methods. Pushyaraga P Venugopal and D. Chakraborty*, J. Biomol. Struct. Dyn. , 40, 5112- 5127, (2022).
Structural and dynamical properties of water in surfactant-like peptide-based nanotubes: Effect of pore size, tube length and charge. Dilip H. N. and D. Chakraborty*, J. Mol. Liq., 323, 115033 (2021).
Effective Inhibition of Mild Steel Corrosion by 6-bromo-(2,4-dimethoxyphenyl) methylidene] imidazo [1,2-a] pyridine-2-carbohydrazide in 0.5 M HCl : Insights from Experimental and Computational study. Vranda Shenoy K; Pushyaraga P Venugopal; Reena Kumari P D*; D. Chakraborty* , J. Mol. Struc., 1232, 130074 (2021).
Diverse interactions of aggregated insulin with selected coumarin dyes: time dependent fluorogenicity, simulation studies and comparison with thioflavin T. S. Dalal, B. K. Das, M. Saini, D. Chakraborty* and K. K Sadhu*, Dyes Pigm., 184, 108796 (2021).
In-silico epitope identification and design of Uricase mutein with reduced immunogenicity. A. K. Nelapati, B. K. Das , J. B. PonnanEttiyappan, D. Chakraborty*, Process Biochemistry, 92, 288- 302 (2020).
Structural and Thermophysical Anomalies of Liquid Water: A Tale of Molecules in the Instantaneous Low- and High-Density Regions. A. Biswas, A. Priyadarsini, D. Chakraborty∗, and B. S. Mallik*, J. Phys. Chem. B., 124,1071-1081 (2020).
Effect of cosolvents in the preferential binding affinity of water in aqueous solutions of amino acids and amides. Dilip H. N. and D. Chakraborty*, J. Mol. Liq., 300, 112375 (2020).
Effect of hydrophobic and hydrogen bonding interactions on the potency of -alanine analogs of G- protein coupled glucagon receptor inhibitors. Pushyaraga P Venugopal, B. K. Das and D. Chakraborty*, Proteins, 88, 327-344 (2020).
Hydrophilicity of the hydrophobic group: Effect of cosolvents and ions. Dilip H. N. and D. Chakraborty*, J. Mol. Liq., 280, 389-398(2019).
Computational insights into factor affecting the potency of diaryl sulfone analogs as Escherichia coli dihydropteroate synthase inhibitors. B. K. Das, Pushyaraga P V and D. Chakraborty*, Comp. Bio. and Chem., 78, 37-52 (2019).
Carbohelicenes and thiahelicene from phthalaldehydes through Perkin approach. P. Sarkar*, B. K. Das, D. Chakraborty, K. Muthamma, J. Mol. Struc., 1195, 309-314 (2019).
Interstitial voids and resultant density of liquid water: A first-principles molecular dynamics study. S. Biswas, D. Chakraborty*, and B. S. Mallik*, ACS Omega, 3, 2010 (2018).