Selected publications (for a complete list, please see the Google Scholar page)
In reverse chronological order:
# equal contributions
* corresponding author
1. Rui PP Neves#, João TS Coimbra#, Pedro Paiva#, Umberto Raucci#, Sudip Das#, Ana Rita Calixto#, António JM Ribeiro#, João PM Sousa#, Pedro Ferreira#, Enrico Trizio, Pedro A Fernandes, Michele Parrinello* and Maria J Ramos*, Methods for the establishment of enzymatic mechanisms - from QM to ML, Chemical Science 2026 (in press).
2. Sudip Das, Umberto Raucci, Enrico Trizio, Peilin Kang, Rui P. P. Neves, Maria J. Ramos and Michele Parrinello, A Machine Learning-Driven Probability-Based Approach to Enzyme Catalysis, ACS Catalysis 2025, 15, 11, 9785-9792.
3. Sudip Das, Umberto Raucci, Rui P. P. Neves, Maria J. Ramos and Michele Parrinello, Correlating Enzymatic Reactivity for Different Substrates using Transferable Data-Driven Collective Variables, PNAS 2024, 121, 49, e2416621121.
4. Dhiman Ray*, Sudip Das*, Umberto Raucci*, Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations, Journal of Chemical Information and Modeling 2024, 64, 9, 3953–3958 (virtual special issue: “Modeling Reactions from Chemical Theories to Machine Learning”).
5. Sudip Das, Umberto Raucci, Rui P. P. Neves, Maria J. Ramos and Michele Parrinello, How and When Does an Enzyme React? Unraveling α-Amylase Catalytic Activity with Enhanced Sampling Techniques, ACS Catalysis 2023, 13, 12, 8092–8098.
6. Aparna Dongre#, Sudip Das#, Ashutosh Bellure, Sanjeev Kumar, Anusha Chandra, Tarak Karmakar, Padmanabhan Balaram, S. Balasubramanian and Hemalatha Balaram, Structural basis for the hyperthermostability of an archaeal enzyme induced by succinimide formation, Biophysical Journal 2021, 120 (17), 3732-3746 (experimental collaboration)(Highlighted as “New and Notable”).
7. Sudip Das, Sudarshan Behera and S. Balasubramanian, Orientational Switch of the Lipase A Enzyme at the Oil-Water Interface: An Order of Magnitude Increase in Turnover Rate with a Single Surfactant Tag Explained, The Journal of Physical Chemistry Letters 2020, 11, 8, 2977-2982 (Selected for Presentation in ACS Spring Meeting 2020).
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