List Of Research Publications (only in Peer-reviewed
Journals)
70. Abhisek Bera, Shreya Mukherjee, and Niladri Patra. Catalytic Chronicle of Thrombin: Investigating Reaction Mechanism and Free Energy Landscapes using QM/MM-Metadynamics Simulations, Submitted
69. Gourav Chakraborty, Niladri Patra, Divergent Interconversion Pathways of Monomeric αSynuclein: Kinetic Insights into Early-Stage Amyloidogenic Conversion across Pathological Isoforms, Submitted
68. P. Negi,....Niladri Patra, and Sumanta Kmar Sahu, Rationally engineered Upconversion Metal Phenolic Nanoprobe for NIR driven multifaceted ROS generation and dual drug delivery: in vitro assay on Human Cervical Cancer, Submitted
67. Kousik K. Bhanja, Rajesh Ghosh, and Niladri Patra. pH-dependent Conformational switching of DICI, DICO, and DOCO starting states of T790M/L858R and T790M/L858R/C797S mutant towards HRD-motif His835 motif. Submitted
66. Kousik K. Bhanja, Rajesh Ghosh, and Niladri Patra. Conformational State Ensembles and Covalent Ligand–Dependent Kinetic Modulation of EGFR Exon 19 Mutants Characterized by Markov State Models, Submitted
65. Sunidhi Raj and Niladri Patra. Exploring the Photovoltaic Potential of BaXS₃ (X = Zr, Hf) Perovskites: A DFT and SCAPS-1D Simulation Study, Submitted
64. Shreya Mukherjee, Diship Srivastava, and Niladri Patra. A Hybrid method for Protein-DNA binding Energy Estimation. Submitted
63. Kunal Dhankhar, Gourav Chakraborty, Abhishek Bera, Arnab Chowdhary, Anupam Bandyopadhyay, Narayan C Mishra, Niladri Patra, Saugata Hazra. Structural insights into the mechanism of C3 side chain fragmentation in cephalosporins with SME-1 class A carbapenemase. Submitted.
62. Kousik K. Bhanja and Niladri Patra. Computational Investigation of the Binding Mechanism and Conformational landscape of Selective Covalent Inhibitors in EGFR exon 19 Deletion and Point Mutations. Submitted.
61. Rajesh Ghosh, Kousik Kumar Bhanja, and Niladri Patra.
Mutation-Driven Remodeling of the LRRK2 Kinase Free-Energy Landscape and Its Consequences for Conformational Transitions and Inhibitor Binding Affinity.J. Chem. Inf. Model. 2026, XX, XX, XXX–XXX60. Sudipta; Basu, Debayan; Chakraborty, Gourav; Patra, Niladri; Nayek, Hari Pada. Element-Ligand Cooperativity of Hypervalent Organotin(IV) Compounds in Hydroboration Reaction of Carbonyl Compounds Chakraborty,
Inorganic Chemistry, ASAP59. Shreya Mukherjee and Niladri Patra.
Elucidating the Role of Protein–Protein Interactions in Modulating Inhibitor Affinity and Release Mechanisms in Serine Arginine Protein Kinase. J. Phys. Chem. B 2026, 130, 9, 2554–2570.
58. Diship Srivastava, Shreya Mukherjee, Muskan Begom, and Niladri Patra.
Effect of Cholesterol on the Gramicidin A Induced Membrane Curvature and Order Parameter.ChemPhysChem, 2026; 27:e202500755.57. Gourav Chakraborty and Niladri Patra.
A Hybrid OPES-eABF Framework for Efficient Exploration and Data-Driven Collective Variable Discovery in Complex Free Energy Landscapes. J. Chem. Inf. Model. 2026, 66, 1, 554–56656. Gourav Chakraborty, Niladri Patra. Dual Allosteric and Orthosteric Inhibition of 14-3-3ζ–α-Synuclein Interaction: A Multiscale Simulation and Machine Learning Approach.
Adv. Theory Simul., 2026, 9:e0145554. Shreya Mukherjee, Abhishek Bera, and Niladri Patra.
Exploring the Structural Dynamics of SRPK1 to Identify Competitive Inhibitors via Molecular Modelling Techniques. ChemPhysChem, 2025, 00, e20250020453. S. Paul, V. Talukdar, D. Srivastava, N. Patra, P. Das. Arylthianthrenium Salts Enabled Palladium-Catalyzed Regioselective Arylation: Access to Value-added 7-Azaindoles,
Org. Lett. 2025, 27, 36, 9987–9992.51.
Gourav Chakraborty, Upasana Deka, Niladri Patra. Mechanistic Insights into Ligand-Mediated Modulation of 14-3-3η/Parkin Interaction through Molecular Dynamics and Enhanced Sampling Simulations. J. Phys. Chem. B 2025, 129, 35, 8902–8918
49. D. Basu, S. Chakraborty, B. Ghosh, S. Mukherjee, N. Patra and H. P. Nayek. Hypervalent Organotin(IV) Compounds as Efficient Catalysts for the Knoevenagel Condensation of Aldehydes. Chem. Asian J. 2025, 20, asia.202500767,
48. 48. D. Basu, S. Chakraborty, G. Chakraborty, S. Bhattacharya, N. Patra and H. P. Nayek, Solvent-free Hydrosilylation of Carbonyl Compounds Catalyzed by Organotin(IV) Compounds.
Dalton Trans. 2025, 54, D5DT01033K47. Gourav Chakraborty, Mahima Sudhir Kolpe, Ambily Nath I.V, Avlokita Tiwari, Praapti Jayaswal, Niladri Patra, Computational structure-guided approach to simulate delamanid and pretomanid binding to mycobacterial F420 redox cycling proteins: identification of key determinants of resistance,
J. Biomol. Struct. Dyn. 2025,1-21.46. Kousik K Bhanja, Niladri Patra.
Identification of Novel Fourth-Generation Allosteric Inhibitors Targeting Inactive State of EGFR T790M/L858R/C797S and T790M/L858R Mutations: A Combined Machine Learning and Molecular Dynamics Approach. J. Phys. Chem. B, 2025, 129, 14, 3610–3629.
45. Gourav Chakraborty, Keka Ojha, Ajay Mandal, Niladri Patra. Optimizing oil detachment from silica surfaces using gemini surfactants and functionalized silica nanoparticles: a combined molecular dynamics and machine learning approach. Phys. Chem. Chem. Phys., 2025,27, 4429-4445.
42. Sk. Akhter, Diship Srivastava, Aman Mishra, Niladri Patra, Pankaj Kumar, Sumanta Padhi, A physicochemical investigation on Cu(II)-based molecular catalysts for the electrochemical reduction of CO2 to syngas. Chem. Eur. J. 2024, e202403321.
41. Kanchan Negi, Ashok Kumar, Gourav Chakraborty, Sudhansubala Sahoo, Niladri Patra, Sumanta Kumar Sahu, Rationally Designed Porous Self-Assembled Nanoparticles for Combinational ChemoPhotodynamic Therapy, Dalton Trans. Dalton Trans., 2024,53, 17465-17479.
40. Rakesh Kumar Roy, Madhur Sharma and Niladri Patraa. SARS-CoV-2 Spike Protein Variants and Bebtelovimab: Immune Escape Mechanisms Revealed by Computational Studies, Phys. Chem. Chem. Phys., 2024,26, 29929-29939.
40.
Abhishek Bera, Pritish Joshi, and Niladri Patra. Delving into Macrolide Binding Affinities and Associated Structural Modulations in Erythromycin Esterase C: Insights into the Venus Flytrap Mechanism. J. Chem. Inf. Model. 2024, 64, 15, 5964–5976.39. Rakesh Roy, Abhishek Bera, Niladri Patra, Insights into Allosteric Inhibition of AcrB Efflux Pump: Role of Distinct Binding Pockets, Protomer Preferences, and Crosstalk Disruption, J. Chem. Inf. Model. 2024, 64, 15, 5964–5976.
38. Gourav Chakraborty, Niladri Patra. Elucidating the Molecular Basis of 14-3-3 Interaction with -Synuclein: Insights from Molecular Dynamics Simulations and the Design of a Novel Protein-Protein Interaction Inhibitor. J. Phys. Chem. B 2024, 128, 29, 7068-7085.
37. Avigyan Naskar, Rakesh Roy, Niladri Patra. Decoding Inhibitor Egression from Wild-Type and G2019S Mutant LRRK2 Kinase: Insights into Unbinding Mechanisms for Precision Drug Design in Parkinsons Disease, J. Phys. Chem. B 2024, 128, 28, 6657–6669.
36. Debayan Basu, Barshali Ghosh, Diship Srivastava, Niladri Patra and Hari Pada Nayek, Mononuclear Organogermanium(IV) Catalysts for [3+2] Cycloaddition Reaction, Dalton Trans., 2024,53, 5648-5657.
35. Abhishek Bera, Shreya Mukherjee, Niladri Patra. Exploring the Transmembrane Allostery in MexB: DB08385 Variant as Promising Inhibitor like Candidate Against Pseudomonas aeruginosa Antibiotic Resistance – A Computational Study, Phys. Chem. Chem. Phys., 2024, 26, 17011-17027.
34. Diship Srivastava, Niladri Patra, Elucidating Daptomycins Antibacterial Efficacy: Insights into the Tripartite Complex with Lipid II and Phospholipids in Bacterial Septum Membrane, J. Phys. Chem. B 2024, 128, 18, 4414–4427.
33. Diship Srivastava, Biswajit Saha, Niladri Patra, Design of Saccharide Based Organic Binder for Low-grade Iron Ore Pelletization using Atomistic Simulations and Machine Learning Methods, J. Mol. Graphics Modell. 2024.
31. Aman Mishra, Diship Srivastava, Niladri Patra, Sumanta Padhi, Formate Dehydrogenase Activity by a Cu(II)-based Molecular Catalyst and Deciphering the Mechanism by DFT studies, Dalton Trans., 2024,53, 1209-1220.
30. Gourav Chakraborty, Ambily Nath I.V, Mukta Sharma, Jigar Sheth, Mahima Korib, Avlokita Tiwari, Niladri Patra, In silico structural and mechanical insights into bedaquiline resistance associated with high-grade non-synonymous mutations in atpE, mmpR5, and pepQ, Journal of Biomolecular Structure & Dynamics, 0, 1-13, 2023.
25. Kousik Kumar Bhanja, Madhur Sharma, Niladri Patra, Uncovering the structural and binding insights of dual inhibitors simultaneously targeting two distinct sites on EGFR kinase, J. Phys. Chem. B 2023, 127, 50, 10749–10765.
24. Avigyan Naskar, Kousik Kumar Bhanja, Rakesh Roy, Niladri Patra, Role of the Residue Q1919 in Increasing Kinase Activity of G2019S LRRK2 Kinase: A Computational Study. ChemPhysChem 2023, e202300306.
23. Rakesh Roy, Abhishek Bera, and Niladri Patra. Encapsulation of testosterone and dihydrotestosterone into chiral carbon nanotubes: A molecular dynamics study. J. Mol. Liq. 376 (2023) 121426.
22. Diship Srivastava and Niladri Patra. Self-Uptake Mechanism of Polymyxin-Based Lipopeptide against Gram-Negative Bacterial Membrane: Role of the First Adsorbed Lipopeptide. J. Phys. Chem. B 2022, 126, 41,8222-8232.
21. Kalipada Manna, Priyapratim Patra, Arpita Roy, Rakesh Kumar Roy, Krishna Chaitanya Sunka, Santanu Dhara, Niladri Patra, Sagar Pal, Amino Acid Inspired Alginate-Based pH Sensitive Polymeric Micelles via Reversible Addition–Fragmentation Chain Transfer Polymerization. ACS Applied Polymer Materials. 2022, 4, 6, 4432-4444.
20. RK Roy, N Patra. Prediction of COMT Inhibitors Using Machine Learning and Molecular Dynamics Methods. J. Phys. Chem. B 2022, 126, 19, 3477–3492.
19. P Bhattacherjee, M Roy, A Naskar, HC Tsai, A Ghosh, N Patra, RP John, Photoinduced generation of the active chloride-phosphate anionophore from its inactive proanionophore. Applied Organometallic Chemistry 36 (1), e6459.
18. Subhasis Dey, Soumya Chatterjee, Anjali Patel, Nirmalya Pradhan, Diship Srivastava, Niladri Patra, Arindam Bhattacharyya, Debasis Manna. Photoresponsive transformation from spherical to nanotubular assemblies: anticancer drug delivery using macrocyclic cationic gemini amphiphiles, Chem. Comm. 57 (38), 4646-4649.
17. Rakesh Roy, Niladri Patra, Configuration Flipping in Distal Pocket of Multidrug Transporter MexB Impacts the Efflux Inhibitory Mechanism, ChemPhysChem, 21 (23), 2516-2524.
16. Priyapratim Patra, Niladri Patra, Sagar Pal, Opposite swelling characteristics through changing the connectivity in a biopolymeric hydrogel based on glycogen and glycine, Polym. Chem. 11, 2630-2634 (2020).
15. Surajit Mondal, Niladri Patra, Hari Nayek, Sumit Hira, Soumit Chatterjee, Swapan Dey, Unusual absence of FRET in triazole bridged coumarin-hydroxyquinoline, an active sensor for Hg2+ detection, Photochem. Photobiol. Sci., 2020,19, 1211-1221.
14. Priyapratim Patra, Venkata Sundeep Seesala, Saundry Raj Soni, Rakesh Kumar Roy, Santanu Dhara, Animesh Ghosh, Niladri Patra, and Sagar Pal. Biopolymeric pH-Responsive Fluorescent Gel for in-vitro and in-vivo Colon Specific Delivery of Metronidazole and Ciprofloxacin; Eur. Polym. J. 114, 255 (2019).
13. Niladri Patra and Alexie V. Tkachenko, Programmable self-assembly of diamond polymorphs from chromatic patchy particles, PRE 98, 032611 (2018).
12. Niladri Patra and Alexie V. Tkachenko, Layer-by-layer Self-assembly of Patchy Particles as a Route to Complex Lattice Structure, PRE 96, 022601 (2017).
11. Niladri Patra, Efthymios I. Loannidis and Heather J. Kulik. Computational Investigation of the Interplay of Substrate Positioning and Reactivity in Catechol O-Methyltransferase. PLOS ONE, 11, 1 (2016).
10. Niladri Patra, Petr Král, and Hossein. R. Sadeghpour. Nucleation and Stabilization of Carbon-Rich Structures in Interstellar media, ApJ, 785, 6 (2014).
9. Irena Yzeiri, Niladri Patra, and Petr Král, Porous Carbon Nanotubes: Molecular Absorption, Transport, and Separation. J. Chem. Phys. 140, 104704 (2014).
8. Niladri Patra, Dominic A. Esan, and Petr Král, Dynamics of Ion Binding to Graphene Nanostructures, J. Phys. Chem. C 117, 10750 (2013), cover page.
7. Ryan M. Pearson, Niladri Patra, Hao-jui Hsu, Sayam Uddin, Petr Král, and Seungpyo Hong, Positively Charged Dendron Micelles Display Negligible Cellular Interactions. ACS Macro Letters 2, 77 (2013).
6. Jin Woo Bae, Ryan M. Pearson, Niladri Patra, Suhair Sunoqrot, Lela Vuković, Petr Král, and Seungpyo Hong, Dendrons-mediated Self-assembly of highly PEGylated block copolymers: a modular nanocarrier platform, Chem. Comm. 47, 10302 (2011).
5. Niladri Patra and Petr Král, Controlled Self-assembly of filled Micelles on Nanotubes, J. Am. Chem. Soc. 133, 6146 (2011).
4. Petr Král, Lela Vuković, Niladri Patra, Boyang Wang, Kyaw Sint, and Alexey Titov, Control of Rotary Motion at the Nanoscale: Motility, actuation, self-assembly, J. Nanosci. Lett., 1, 128, (2011). (Cover page)
3. Niladri Patra, Yuanbo Song, and Petr Král, Self-Assembly of Graphene Nanostructures on Nanotubes, ACS Nano 5, 1798 (2011).
2. Goutam Mukherjee, Niladri Patra, Poranjyoti Barua, and Bhairav Jayaram, Fast Empirical GAFF Compatible Partial Atomic Charge Assignment Scheme for Modeling Interactions of Small Molecules with Biomolecular Targets, J. Comp. Chem. 32, 893 (2010).
1. Niladri Patra, Boyang Wang, and Petr Král, Nanodroplet Activated and Guided Folding of Graphene Nanostructures, Nano Lett. 9, 3766 (2009).
