Dr. Niladri Patra Research Group
Department of Chemistry and Chemical Biology, IIT(ISM) Dhanbad
PUBLICATIONS
50. 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, Journal of Biomolecular Structure & Dynamics, accepted​
​​49. Gourav Chakraborty, Keka Ojha, Ajay Mandal, Niladri Patra, Effect of spacer group variation of gemini surfactants on the detachment of oil from silica surfaces with different hydrophobicity: a molecular dynamics study, Submitted
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48. Shreya Mukherjee, Abhishek Bera, and Niladri Patra. Discovery of Cogent SRPK1 Inhibitor by Employing Molecular Modelling Techniques. Submitted
​​47. Gourav Chakraborty, Niladri Patra. Targeting 14-3-3/-Synuclein Complexation: Identification of Allosteric Sites and Development of Modulatory Inhibitors, Submitted.​​
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46. Kousik K. Bhanja and Niladri Patra, Identification of novel Fourth-Generation Allosteric Inhibitors Targeting EGFR T790M/L858R/C797S and T790M/L858R Mutations: A Combined Machine Learning and Molecular Dynamics Approach. Submitted.​
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45. Diship Srivastava, Shreya Mukherjee, Muskan Begom and Niladri Patra. Modulation of Gramicidin A’s Structural and Dynamical Properties by Cholesterol in the Membrane. Submitted.​​​
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Improving the Computational Efficiency of the Adaptive Biasing Force Sampling by Leveraging the Telescopic-Solvation Scheme.
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Diship Srivastava and Niladri Patra
SARS-CoV-2 Variants and Bebtelovimab: Immune Escape Mechanisms Revealed by Computational Studies.
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Rakesh Roy, Madhur Sharma, Niladri Patra.
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.
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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.
Delving into Macrolide Binding Affinities and Associated Structural Modulations in Erythromycin Esterase C: Insights into the Venus Flytrap Mechanism.
Abhishek Bera, Pritish Joshi, and Niladri Patra
Insights into Allosteric Inhibition of the AcrB Efflux Pump: Role of Distinct Binding Pockets, Protomer Preferences, and Crosstalk Disruption.
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Rakesh Kumar Roy, Abhishek Bera, Niladri Patra
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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.
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Gourav Chakraborty and Niladri Patra
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Decoding Inhibitor Egression from Wild-Type and G2019S Mutant LRRK2 Kinase: Insights into Unbinding Mechanisms for Precision Drug Design in Parkinsons Disease.
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Avigyan Naskar, Rakesh Roy, and Niladri Patra
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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.
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35. Phys. Chem. Chem. Phys., 2024, 26, 17011-17027.
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Exploring the Transmembrane Allostery in MexB: DB08385 Variant as Promising Inhibitor like Candidate Against Pseudomonas aeruginosa Antibiotic Resistance – A Computational Study.
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Abhishek Bera, Shreya Mukherjee, and Niladri Patra
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34. J. Phys. Chem. B 2024, 128, 18, 4414–4427
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Elucidating Daptomycins Antibacterial Efficacy: Insights into the Tripartite Complex with Lipid II and Phospholipids in Bacterial Septum Membrane.
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Diship Srivastava and Niladri Patra
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33. J. Mol. Graphics Modell. 2024, 129,108730.​
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Design of Saccharide Based Organic Binder for Low-grade Iron Ore Pelletization using Atomistic Simulations and Machine Learning Methods.​
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Diship Srivastava, Biswajit Saha, and Niladri Patra
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32. J. Phys. Chem. B 2024, 128, 3, 648–663.​
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Machine Learning-Guided Discovery of AcrB and MexB Efflux Pump Inhibitors.​
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Abhishek Bera, Rakesh Roy, Pritish Joshi, and Niladri Patra,
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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.​​​​​​​​​​​​​​​​
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Probing the pH Sensitivity of OprM: Insights into Metastable States and Semi-Open Conformation, ​
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Rakesh Roy and Niladri Patra,
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Structural insight into G2019S mutated LRRK2 kinase and brain- penetrant Type I inhibitor complex: A Molecular dynamics approach.
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Avigyan Naskar, Kousik Kumar Bhanja, Rakesh Roy, and Niladri Patra
In silico structural and mechanical insights into bedaquiline resistance associated with high-grade non-synonymous mutations in atpE, mmpR5, and pepQ
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Gourav Chakraborty, Ambily Nath I.V, Mukta Sharma, Jigar Sheth, Mahima Korib, Avlokita Tiwari, Niladri Patra
Telescoping-Solvation-Box Protocol based Umbrella Sampling Method for Potential Mean Force Estimation
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Diship Srivastava and Niladri Patra
Enhanced Uptake of Anticancer C6-Pep Dimer in Tumor Membrane Caused by Differential pKa in Acidic Tumor Microenvironment
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Diship Srivastava and Niladri Patra
Uncovering the structural and binding insights of dual inhibitors simultaneously targeting two distinct sites on EGFR kinase
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Kousik Kumar Bhanja, Madhur Sharma, and Niladri Patra
Role of the Residue Q1919 in Increasing Kinase Activity of G2019S LRRK2 Kinase: A Computational Study.
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Avigyan Naskar, Kousik Kumar Bhanja, Rakesh Roy, and Niladri Patra
Encapsulation of testosterone and dihydrotestosterone into chiral carbon nanotubes: A molecular dynamics study.
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Rakesh Roy, Abhishek Bera, and Niladri Patra.
Self-Uptake Mechanism of Polymyxin-Based Lipopeptide against Gram-Negative Bacterial Membrane: Role of the First Adsorbed Lipopeptide.
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Diship Srivastava and Niladri Patra.
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.
Prediction of COMT Inhibitors Using Machine Learning and Molecular Dynamics Methods.
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Rakesh Kumar Roy and Niladri Patra.
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. COVER PICTURE
Configuration Flipping in Distal Pocket of Multidrug Transporter MexB Impacts the Efflux Inhibitory Mechanism
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​​​​​​​​​​​​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).
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13. Niladri Patra and Alexie V. Tkachenko, Programmable self-assembly of diamond polymorphs from chromatic patchy particles, PRE 98, 032611 (2018).
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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).
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Proceedings:
1. Petr Král, Lela Vuković, Niladri Patra, Boyang Wang, and Alexey Titov, Control of Rotary Motion at the Nanoscale: Motility, Actuation, Self-assembly, Proceedings of the Beilstein Symposium on Functional Nanoscience, Bozen, June, 2011.
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2. Niladri Patra, Petr Král, and Hossein. R. Sadeghpour. Dynamics of Synthesis of Large Carbon Structures in Interstellar Medium. Proceedings IAU Symposium 297: The diffuse interstellar bands. Netherlands, May, 2013.
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3. Ryan M Pearson, Jin Woo Bae, Niladri Patra, Suhair Sunoqrot, Sayam Uddin, Lela Vukovic, Petr Král, Seungpyo Hong, Synthesis and self-assembly of highly PEGylated dendron-coils: A potential nanocarrier platform. Cancer Research, Vol. 72, 1954-1954.
Book Chapters:
1. John Russell, Boyang Wang, Niladri Patra, Petr Král, Water Nanodroplets: Molecular Drag and Self-assembly. Nanodroplets, Lecture Notes in Nanoscale Science and Technology, Volume 18 2013, ISBN: 978-1-4614-9471-3.
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All the above manuscripts carry the copyright of the respective publisher and may be downloaded for personal use only. Any other use requires prior permission of the author and the respective publisher.