Dr Kshatresh Dubey
Assistant Professor School of Natural Sciences
School of Natural Sciences
Email: kshatresh.dubey@snu.edu.in
1) De novo Enzyme Designing and Protein engineering 2) Molecular Modelling and Computational drug designing 3) Protein-protein Interactions and Protein-ligand Interactions using a computational approach 4) Molecular Docking, MD Simulations, and Free Energy Calculations 5) Density Functional Theory (...
Research Overview
1) De novo Enzyme Designing and Protein engineering 2) Molecular Modelling and Computational drug designing 3) Protein-protein Interactions and Protein-ligand Interactions using a computational approach 4) Molecular Docking, MD Simulations, and Free Energy Calculations 5) Density Functional Theory (DFT) calculations, QM/MM Calculations and Ab-initio MD simulations using Cp2K Know more: Click here
Education
2013 Ph.D. Deen Dayal Upadhyay Gorakhpur University Gorakhpur 2003 M.Sc. Deen Dayal Upadhyay Gorakhpur University Gorakhpur
Experience
12/12-12/13 Postdoc, Indian Institute of Technology Kanpur, Kanpur India 01/14-09/17 Postdoc, The Hebrew University of Israel, Jerusalem, Israel 10/17-09/18 Senior Researcher, Uppsala University Sweden, Uppsala Sweden 10/18-02/19 Postdoc, University of Barcelona, Barcelona, Spain 03/19-01/22 Ramalingaswami Fellow, Department of Chemistry, School of Natural Sciences, Shiv Nadar University, Delhi-NCR 02/22 ?Present Assistant Professor, Department of Chemistry, School of Natural Sciences, Shiv Nadar University Delhi-NCR, A227B
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| 1 |
Article
Irradiation-driven phase dynamics and surface property evolution in Ni–Si Co-sputtered thin films under swift heavy ion irradiation
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Shah, K.; Maity, G.; Patajoshi, S.; Singh, F.; Sulania, I.; Gupta, M.; Kanjilal, A.; Pandey, R.; Dubey, S. | Applied Surface Science, 719 | 2026 | 0 |
| 2 |
Article
Biofuel Production by Aldehyde-Deformylating Oxygenase: Insights into Spin States, Spin Coupling, and Diiron Cofactor Reactivity Using Multiscale Modeling
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Rana, T.R.K.; Singh, D.; Nath, R.; Paul, A.; Dutta Dubey, K.D.; Rajaraman, G. | Inorganic Chemistry, 65(2), 1561-1573 | 2026 | 0 |
| 3 |
Book chapter
Addressing the Challenges in Federating Edge Resources
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Dubey, A.; Sharma, S.; Devi, K.; Singh, S.P.; Balusamy, B.; Samuel, P. | Advances in Science, Technology and Innovation, Part F1277, 17-33 | 2026 | 0 |
| 4 |
Book chapter
A Lightweight AI-Enabled Container Middleware for Edge Cloud Architectures
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Kumar, N.; Sharma, S.; Dubey, A.; Devi, K.; Balusamy, B. | Advances in Science, Technology and Innovation, Part F1277, 75-99 | 2026 | 0 |
| 5 |
Book chapter
Predictive Analysis in Healthcare to Support Fog Application Deployment
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Kumar, N.; Sharma, S.; Dubey, A.; Saini, V.; Jaiprakash, S.P.; Balusamy, B. | Advances in Science, Technology and Innovation, Part F1277, 111-122 | 2026 | 0 |
| 6 |
Review Open access
Role of Propionate Side Chain in Heme-Containing Metalloenzymes
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Singh, D.; Kardam, V.; Dutta Dubey, K.D. | ACS Organic and Inorganic Au, 5(6), 451-466 | 2025 | 0 |
| 7 |
Article Open access
Oriented Electric Fields─Universal Catalysts
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Shaik, S.; Danovich, D.; Kalita, S.; Dutta Dubey, K.D. | Accounts of Chemical Research, 58(19), 3071-3080 | 2025 | 2 |
| 8 |
Article
Unusually Stable Synthetic Diheme Bis-Fe(IV)oxo: An Intermediate in Diheme Enzymes MauG and BthA
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Samanta, D.; Sarkar, S.; Singh, D.; Samanta, S.; Manna, S.; Dutta Dubey, K.D.; Dey, A.; Shaik, S.; Rath, S.P. | Journal of the American Chemical Society, 147(26), 22562-22571 | 2025 | 1 |
| 9 |
Article
Efficient Access of Heterocycles Utilizing Inherent Carbodicationic Reactivity of Ynone via Lewis Acid Catalysed C─C Triple Bond Cleavage
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Ahmad, A.; Indu, K.; Siddiqui, S.A.; Gupta, L.; Dutta Dubey, K.D.; Kapat, A. | Chemistry - A European Journal, 31(32) | 2025 | 0 |
| 10 |
Article
Leveraging molecular dynamics, physicochemical, and structural analysis to explore OMP33-36 protein as a drug target in Acinetobacter baumannii: An approach against nosocomial infection
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Singh, S.; Agarwal, J.; Das, A.; Trivedi, M.; Dutta Dubey, K.D.; Athish Pranav, K.V.; Dwivedi, M. | Journal of Molecular Graphics and Modelling, 136 | 2025 | 1 |
| 11 |
Article
Adaptive adam-based optimizers using second-order weight decoupling and gradient-aware weight decay for vision transformer
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Hemanth Sai, B.; Mukherjee, S.; Dubey, S.R. | Machine Vision and Applications, 36(3) | 2025 | 1 |
| 12 |
Article
Synthesis ADMET molecular docking, MD simulation and MM-PBSA investigations of a novel hetero-steroid with Anti-proliferative and Anti-inflammatory properties
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Srivastava, S.; Pandey, S.; Kumar, A.; Siddiqui, S.A.; Dutta Dubey, K.D. | Journal of Molecular Structure, 1321 | 2025 | 6 |
| 13 |
Article
The Role of the Carbonyl Group in C-C Triple Bond Cleavage of Ynones via Grob-Type Fragmentation under Acidic Conditions
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Ahmad, A.; Siddiqui, S.A.; Tyagi, P.; Gupta, L.; Dutta Dubey, K.D.; Kapat, A. | Journal of Organic Chemistry | 2025 | 1 |
| 14 |
Article Open access
Structure-Based Discovery of MolPort-137: A Novel Autotaxin Inhibitor That Improves Paclitaxel Efficacy
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Rai, P.; Clark, C.J.; Kardam, V.; Womack, C.B.; Thammathong, J.; Norman, D.D.; Tigyi, G.J.; Bicker, K.; Weissmiller, A.M.; Dutta Dubey, K.D.; Banerjee, S. | International Journal of Molecular Sciences, 26(2) | 2025 | 0 |
| 15 |
Article
Development of nano-porous Au thin film at room temperature via ion irradiation in a-Ge/Au bilayer system followed by chemical etching of Ge
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Maity, G.; Patel, G.; Ojha, S.; Dubey, S.; Patel, S.P.; Kanjilal, D. | Journal of Crystal Growth, 649 | 2025 | 1 |
| 16 |
Article
Amyloid-like Aggregation Propensities of Metabolites- Homogentisic Acid, N-Acetyl Aspartic Acid and Isovaleric Acid
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Dave, R.; Jaiswal, A.; Naseer, A.; Tripathi, A.; Patel, M.; Revi, N.; Rengan, A.K.; Dutta Dubey, K.D.; Nazir, A.; Verma, S.; Gour, N. | ChemBioChem, 25(23) | 2024 | 2 |
| 17 |
Article
Structural and mechanistic insights into oxidative biaryl coupling to form the arylomycin core by an engineered CYP450
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Kardam, V.; Bhatt, V.; Dutta Dubey, K.D. | Dalton Transactions, 54(2), 754-763 | 2024 | 4 |
| 18 |
Article
Mechanism of a novel metal-free carbonic anhydrase
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Yadav, S.; Kalita, S.; Dutta Dubey, K.D. | Physical Chemistry Chemical Physics, 26(44), 28124-28132 | 2024 | 3 |
| 19 |
Article
Designed CYP450 Scaffold That Possesses a Local Electric Field Biodegrades Polyethylene Terephthalate
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Siddiqui, S.A.; Shaik, S.; Dutta Dubey, K.D. | ACS Catalysis, 14(20), 15108-15122 | 2024 | 4 |
| 20 |
Article
Understanding the Functional Dynamics of the TokK Enzyme in Carbapenem Biosynthesis via MD Simulations and QM/MM Calculations
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Siddiqui, S.A.; Dutta Dubey, K.D. | Inorganic Chemistry, 63(40), 18963-18971 | 2024 | 1 |
| 21 |
Article Open access
Computational investigation of novel synthetic analogs of C-1′β substituted remdesivir against RNA-dependent RNA-polymerase of SARS-CoV-2
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Cardoza, S.; Singh, A.; Sur, S.; Singh, M.; Dutta Dubey, K.D.; Samanta, S.K.; Mandal, A.; Tandon, V. | Heliyon, 10(17) | 2024 | 2 |
| 22 |
Review
Advances in borophene based photodetectors for a sustainable tomorrow: a comprehensive review
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Maity, G.; Mishra, P.K.; Patel, G.; Dubey, S. | Nanoscale, 16(39), 18295-18318 | 2024 | 8 |
| 23 |
Book chapter
Concept and applications of biomolecular simulations
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Kardam, V.; Dutta Dubey, K.D. | Computational Studies: From Molecules to Materials, 87-115 | 2024 | 0 |
| 24 |
Article Open access
Structural assessment of OsNIP2;1 highlighted critical residues defining solute specificity and functionality of NIP class aquaporins
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Sharma, Y.; Thakral, V.; Raturi, G.; Dutta Dubey, K.; Sonah, H.; Pareek, A.; Sharma, T.R.; Deshmukh, R. | Journal of Advanced Research, 58, 1-11 | 2024 | 3 |
| 25 |
Article Open access
On the engineering of reductase-based-monooxygenase activity in CYP450 peroxygenases
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Yadav, S.; Shaik, S.; Dutta Dubey, K. | Chemical Science, 15(14), 5174-5186 | 2024 | 7 |
| 26 |
Article
Deep Model Compression based on the Training History
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Basha, S.H.S.; Farazuddin, M.; Pulabaigari, V.; Dubey, S.R.; Mukherjee, S. | Neurocomputing, 573 | 2024 | 19 |
| 27 |
Article
Amyloidogenic Propensity of Metabolites in the Uric Acid Pathway and Urea Cycle Critically Impacts the Etiology of Metabolic Disorders
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Patel, M.; Jaiswal, A.; Naseer, A.; Tripathi, A.; Joshi, A.; Minocha, T.; Kautu, A.; Gupta, S.; Ballabh Joshi, K.B.; Pandey, M.K.; Kumar, R.; Dutta Dubey, K.; Nazir, A.; Verma, S.; Gour, N. | ACS Chemical Neuroscience, 15(5), 916-931 | 2024 | 6 |
| 28 |
Article Open access
Fetal Ultrasound Segmentation and Measurements Using Appearance and Shape Prior Based Density Regression with Deep CNN and Robust Ellipse Fitting
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Dubey, G.; Srivastava, S.; Jayswal, A.K.; Saraswat, M.; Singh, P.; Memoria, M. | Journal of Imaging Informatics in Medicine, 37(1), 247-267 | 2024 | 5 |
| 29 |
Conference paper
WSD: Wild Selfie Dataset for Face Recognition in Selfie Images
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Kumarapu, L.; Dubey, S.R.; Mukherjee, S.; Mohan, P.; Vinnakoti, S.P.; Karthikeya, S. | Communications in Computer and Information Science, 2009 CCIS, 1-12 | 2024 | 2 |
| 30 |
Article
Phytocompounds as versatile drug-leads targeting mProtease in the SARS-CoV-2 virus: insights from a molecular dynamics study
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Dwivedi, M.; Devi, S.S.; Singh, S.; Trivedi, M.; Hussain, N.; Yadav, S.; Dutta Dubey, K. | Journal of Biomaterials Science, Polymer Edition, 35(16), 2528-2548 | 2024 | 2 |
| 31 |
Article
The mechanistic insights into different aspects of promiscuity in metalloenzymes
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Tripathi, A.; Dutta Dubey, K. | Advances in Protein Chemistry and Structural Biology, 141, 23-66 | 2024 | 1 |
| 32 |
Editorial Open access
Editorial: Computational aspects of biomolecular recognition and processes
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Srivastava, A.K.; Karnati, K.R.; Dutta Dubey, K. | Frontiers in Chemistry, 12 | 2024 | 0 |
| 33 |
Article Open access
Rational design of a cyclohexanone dehydrogenase for enhanced α,β-desaturation and substrate specificity
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Singh, W.; Brown, N.L.; McCue, H.V.; Marriott, S.R.; Wilson, R.C.; Perry, J.; Turkenburg, J.P.; Dutta Dubey, K.; Prior, S.H.; Carnell, A.J.; Taylor, E.J.; Black, G.W. | Chemical Science | 2024 | 2 |
| 34 |
Review Open access
Designed Local Electric Fields─Promising Tools for Enzyme Engineering
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Siddiqui, S.A.; Stuyver, T.; Shaik, S.; Dutta Dubey, K. | JACS Au, 3(12), 3259-3269 | 2023 | 35 |
| 35 |
Article Open access
Computationally guided bioengineering of the active site, substrate access pathway, and water channels of thermostable cytochrome P450, CYP175A1, for catalyzing the alkane hydroxylation reaction
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Taher, M.; Dutta Dubey, K.; Mazumdar, S. | Chemical Science, 14(48), 14316-14326 | 2023 | 14 |
| 36 |
Article
Novel template free synthesis of high surface area mesoporous ceria and adaptive neuro fuzzy interference system (ANFIS) modelling for Cr(VI) adsorption
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Dubey, M.; Joshi, M.; Thota, C.; Kumar, R. | Materials Science and Engineering: B, 298 | 2023 | 7 |
| 37 |
Article Open access
Unraveling topoisomerase IA gate dynamics in presence of PPEF and its preclinical evaluation against multidrug-resistant pathogens
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Maurya, V.; Singh, R.; Singh, R.K.; Pandey, S.; Yadav, P.; Parashar, P.; Gaind, R.; Dutta Dubey, K.D.; Patwari, G.; Tandon, V. | Communications Biology, 6(1) | 2023 | 6 |
| 38 |
Article
Tyr 118-Mediated Electron Transfer is Key to the Chlorite Decomposition in Heme-Dependent Chlorite Dismutase
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Kardam, V.; Dutta Dubey, K.D. | Inorganic Chemistry, 62(44), 18322-18330 | 2023 | 6 |
| 39 |
Article Open access
Design and Synthesis of Co-initiators via Base-Catalysed Sequential Conjugate Addition: Application in Photoinduced Radical Polymerisation Reaction
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Ahmad, A.; Siddiqui, S.A.; Mittal, G.; Sukumar, N.; Dutta Dubey, K.D.; Kapat, A. | Chemistry - A European Journal, 29(57) | 2023 | 1 |
| 40 |
Review
Nanomachines in living matters: the soft-robot cytochrome P450
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Shaik, S.; Dutta Dubey, K.D. | Trends in Chemistry, 5(10), 763-774 | 2023 | 7 |
| 41 |
Article Open access
A porphyrin-based molecular cage guided by designed local-electric field is highly selective and efficient
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Siddiqui, S.A.; Shaik, S.; Kalita, S.; Dutta Dubey, K.D. | Chemical Science, 14(37), 10329-10339 | 2023 | 8 |
| 42 |
Article Open access
Electro-Freezing of Supercooled Water Is Induced by Hydrated Al3+ and Mg2+ Ions: Experimental and Theoretical Studies
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Fuhrman Javitt, L.; Kalita, S.; Dutta Dubey, K.D.; Ehre, D.; Shaik, S.; Lahav, M.; Lubomirsky, I. | Journal of the American Chemical Society, 145(34), 18904-18911 | 2023 | 10 |
| 43 |
Article Open access
Esterase Specific Fluorescent Probe: Mechanistic Understanding Using QM/MM Calculation and Cell States Discrimination
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Yadav, R.; Munan, S.; Kardam, V.; Dutta Dubey, K.D.; Samanta, A. | Chemistry - A European Journal, 29(32) | 2023 | 13 |
| 44 |
Article
Substrate Conformation Regulates Aromatic C-H Vs C-F Bond Activation in Heme-Dependent Tyrosine Hydroxylase
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Singh, W.; Santos, S.F.G.; Yadav, S.; Black, G.W.; Dutta Dubey, K.D. | Biochemistry, 62(10), 1577-1587 | 2023 | 5 |
| 45 |
Article
A single site mutation can induce functional promiscuity in homoserine kinase
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Tripathi, A.; Dutta Dubey, K.D. | Organic and Biomolecular Chemistry, 21(22), 4648-4655 | 2023 | 4 |
| 46 |
Article
Decarboxylation and Protonation Enigma in the H85Q Mutant of Cytochrome P450OleT
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Yadav, S.; Shaik, S.; Dutta Dubey, K.D. | Journal of Physical Chemistry B, 127(13), 2927-2933 | 2023 | 6 |
| 47 |
Article
A Note on Linear Complementarity via Two-Person Zero-Sum Games
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Dubey, D.; Neogy, S.K.; Raghavan, T.E.S. | International Game Theory Review, 25(1) | 2023 | 0 |
| 48 |
Article Open access
How Can Static and Oscillating Electric Fields Serve in Decomposing Alzheimer's and Other Senile Plaques?
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Kalita, S.; Bergman, H.; Dutta Dubey, K.D.; Shaik, S. | Journal of the American Chemical Society, 145(6), 3543-3553 | 2023 | 24 |
| 49 |
Article
Drug review sentimental analysis based on modular lexicon generation and a fusion of bidirectional threshold weighted mapping CNN-RNN
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Dubey, G.; Singh, H.P.; Sheoran, K.; Dhand, G.; Malik, P. | Concurrency and Computation: Practice and Experience, 35(3) | 2023 | 13 |
| 50 |
Book chapter
Earth observation applications for urban mapping and monitoring: research prospects, opportunities and challenges
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Chauhan, A.; Wasim, M.; Mohanty, S.; Pandey, P.C.; Pandey, M.; Maurya, N.K.; Rankavat, S.; Dubey, S.B. | Earth Observation in Urban Monitoring: Techniques and Challenges, 197-229 | 2023 | 3 |
Project details will be updated soon.
Research contributions aligned with UN Sustainable Development Goals:
3
Good Health and Well-being
6
Clean Water and Sanitation
7
Affordable and Clean Energy
9
Industry, Innovation and Infrastructure
11
Sustainable Cities and Communities
13
Climate Action
| Type | Title | Status | Filed Date | Inventors |
|---|---|---|---|---|
| No patents available. | ||||
Awards & Honors
- 2011 Senior Research Fellowship (CSIR) 2014 PBC Fellowship for outstanding postdocs 2017 Sven and Lilly Fellowship, Sweden 2018 Ramalingaswami re-entry fellowship
Professional Memberships
- No memberships listed.
Additional information will be updated soon.