NANDAN KUMAR

Publications

My work spans AI/ML for peptides and proteins, molecular simulations and non-covalent interactions, and food protein structure and functionality. Below is a complete list of manuscripts, peer-reviewed articles, book chapters, and patent.

Citation metrics (Google Scholar, since 2020): Citations ≈ 280 · h-index = 10 · i10-index = 10. A live list is available on Google Scholar .

30+
Publications
3
Manuscripts
in progress
7
Book
chapters
1
Patent
Manuscripts Journal articles Book chapters Patent

Selected highlights

AI / ML
pLM4CPPs: Protein Language Model-Based Predictor for Cell Penetrating Peptides
Kumar, N.; Du, Z.; Li, Y. J. Chem. Inf. Model., 2025, 65, 1128.
doi
Membranes
Membrane Selectivity Mechanisms of the Antimicrobial Peptide Snakin-Z Against Prokaryotic and Eukaryotic Membrane Models
Kumar, N.; Du, Z.; Amachawadi, R. G.; Guo, X.; Zhao, J.; Li, Y. J. Phys. Chem. B, 2025, 129, 4409.
doi
Food proteins
Solvent-dependent structural and dynamic behavior of α-gliadin in aqueous ethanol systems: Insights from molecular dynamics simulations
Kumar, N.; Li, Y. Food Chemistry, 2025, 497, 147044.
doi
Non-covalent
Towards Developing a Criterion to Characterize Non-Covalent Bonds
Kumar, N.; Saha, S.; Sastry, G. N. Phys. Chem. Chem. Phys., 2021, 23(14), 8478.
doi
Databases
Analyzing the Aromatic–Aromatic Interactions in Proteins: A2ID 2.0
Kumar, Y. B.; Kumar, N.; Vaikundamani, S.; et al. Int. J. Biol. Macromol., 2023, 127207.
doi
Review
Comprehensive review of chickpea (Cicer arietinum): Nutritional significance, health benefits, techno‐functionalities, and food applications
Kumar, N.; Hong, S.; Zhu, Y.; et al. Compr. Rev. Food Sci. Food Saf., 2025, 24, e70152.
doi

Manuscripts submitted / under preparation

[1]
pLM4G-CPPs: Protein Language Model-Guided Graph Learning for Cell-Penetrating Peptides Prediction
Kumar, N.; Li, Y. 2026. (Under preparation)
[2]
Concentration-Dependent Mechanisms of Melittin-Induced Pore Formation in Eukaryotic and Prokaryotic Membranes
Kumar, N.; Li, Y. 2026. (Under preparation)
[3]
All-atom to Coarse-grained Simulations of Food Proteins: Principles, Force fields, and Applications
Kwon, H.; Kumar, N.; Comer, J; Li, Y. Food Chemistry, 2026, (Under revision)

Peer-reviewed journal articles

[4]
Solvent-Dependent Structural and Dynamic Behavior of α-Gliadin in Aqueous Ethanol Systems: Insights from Molecular Dynamics Simulations
Kumar, N.; Li, Y. Food Chemistry, 2025, 497, 147044.
doi
[5]
Ferrichrysin Siderophore from Gangetic Aspergillus japonicus: Isolation, Characterization, and Role in Sustained Arsenic Tolerance
Singh, A.; Kumar, R.; Kumar, N.; Barvkar, V. T.; Kumari, S.; Kumar, Y. B.; Pable, A. A.; Shukla, E.; Srivastava, A. World Journal of Microbiology and Biotechnology, 2025, 41, 477.
doi
[6]
Modification of Structural Properties and Potential Allergenicity of Ovalbumin Induced by Ultrasound Treatment During in vitro Digestion
Yang, J.; Kumar, N.; Kuang, H.; Li, Y.; Song, J. Food Chemistry, 2025, 493, 146015.
doi
[7]
Membrane Selectivity Mechanisms of Antimicrobial Peptide Snakin-Z against Prokaryotic and Eukaryotic Membrane Models
Kumar, N.; Du, Z.; Amachawadi, R. G.; Guo, X.; Zhao, J.; Li, Y. J. Phys. Chem. B, 2025, 129, 4409.
doi
[8]
pLM4CPPs: Protein Language Model-Based Predictor for Cell Penetrating Peptides
Kumar, N.; Du, Z.; Li, Y. J. Chem. Inf. Model., 2025, 65, 1128.
doi
[9]
Comprehensive Review of Chickpea (Cicer arietinum): Nutritional Significance, Health Benefits, Functionalities, and Food Applications
Kumar, N.; Hong, S.; Zhu, Y.; Garay, A.; Yang, J.; Henderson, D.; Zhang, X.; Xu, Y.; Li, Y. Compr. Rev. Food Sci. Food Saf., 2025, 24, e70152.
doi
[10]
Changes of Digestive Stability and Potential Allergenicity of High Hydrostatic Pressure-Treated Ovalbumin During in vitro Digestion
Yang, J.; Kumar, N.; Kuang, H.; Song, J.; Li, Y. Food Chemistry, 2025, 473, 142962.
doi
[11]
Changes of Structure Properties and Potential Allergenicity of Ovalbumin under High Hydrostatic Pressures
Yang, J.; Kuang, H.; Kumar, N.; Song, J.; Li, Y. Food Research International, 2024, 190, 114658.
doi
[12]
Pea Protein-Stabilized Emulsion as a High-Performance Cryoprotectant in Frozen Dough: Effects on the Strong Stability and Baking Performance
Chen, Y.; […]; Kumar, N.; […]; Zhu, X. Foods, 2024, 13, 3840.
doi
[13]
Co-Stabilization Effects of Gluten/Carrageenan to the Over-Heated Myofibrillar Protein: Inhibit the Undesirable Gel Weakening and Protein Over-Aggregations
Zhu, X.; […]; Kumar, N.; Li, Y.; […]; Dong, Z. Int. J. Biol. Macromol., 2024, 282, 136722.
doi
[14]
Molecular Property Diagnostic Suite for COVID-19 (MPDS COVID-19): An Open Access Disease-Specific Drug Discovery Portal
Priyadarshinee, L.; […]; Kumar, N.; […]; Sastry, G. N. GigaByte, 2024, 1–17.
doi
[15]
Analyzing the Aromatic–Aromatic Interactions in Proteins: A2ID 2.0
Kumar, Y. B.; Kumar, N.; Vaikundamani, S.; Nagamani, S.; Mahanta, H. J.; Sastry, G. M.; Sastry, G. N. Int. J. Biol. Macromol., 2023, 127207.
doi
[16]
Analyzing the Cation–Aromatic Interactions in Proteins: Cation-Aromatic Database V2.0
Kumar, Y. B.; Kumar, N.; John, L.; Mahanta, H. J.; Vaikundamani, S.; Nagamani, S.; Sastry, G. M.; Sastry, G. N. Proteins, 2023, 92, 179–191.
doi
[17]
Molecular Property Diagnostic Suite Compound Library (MPDS-CL): A Structure Based Classification of the Chemical Space
Jhon, L.; […]; Kumar, N.; […]; Sastry, G. N. Molecular Diversity, 2023. (Under revision)
preprint
[18]
Tracing the Transition from Covalent to Non-Covalent Functionalization of Pyrene through C-, N-, and O-Based Ionic and Radical Substrates Using Quantum Mechanical Calculations
Pandey, A.;* Kumar, N.* RSC Advances, 2023, 13, 14119.
doi
[19]
First Principle Calculations on the Micro-Solvation of 3d-Transition Metal Ions: Solvation vs Splitting Water
Kumar, Y. B.; Kumar, N.; Sharma, H.; Sastry, G. N. Theor. Chem. Acc., 2023, 142, 35.
doi
[20]
Binding Propensity and Selectivity of Cationic, Anionic and Neutral Guests with Model Hydrophobic Hosts: A First Principles Study
Kumar, Y. B.; Pandey, A.; Kumar, N.; Sastry, G. N.* J. Comput. Chem., 2022, 1–10.
doi
[21]
Towards Systematic Exploration of Chemical Space: Building the Fragment Library Module in Molecular Property Diagnostic Suite
Gaur, A. S.; John, L.; Kumar, N.; Vivek, R. M.; Nagamani, S.; Mahanta, H. J.; Sastry, G. N. Molecular Diversity, 2022, 1–10.
doi
[22]
6-Ethoxy-4-N-(2-Morpholin-4-Ylethyl)-2-N-Propan-2-yl-1,3,5-Triazine-2,4-Diamine Endows Herbicidal Activity Against Phalaris Minor a Weed of Wheat Crop Field: An in-Silico and Experimental Approaches of Herbicide Discovery
Kumar, N.; Rani, P.; Agarwal, S.; Singh, D. V. J. Mol. Model., 2022, 28, 77.
doi
[23]
Repurposing of Approved Drugs to Predict New Inhibitors for Viral Infectious Diseases: A Molecular Modelling Approaches
Kumar, N.; Sharma, H.; Sastry, G. N. J. Biomol. Struct. Dyn., 2022, 40, 8056–8073.
doi
[24]
Towards Developing a Criterion to Characterize Non-Covalent Bonds: A Quantum Mechanical Study
Kumar, N.; Saha, S.; Sastry, G. N. Phys. Chem. Chem. Phys., 2021, 23(14), 8478.
doi
[25]
Fate of Sc-Ion Interaction with Water: A Computational Study to Address Splitting Water Versus Solvating Sc Ion
Kumar, N.; Kumar, Y. B.; Sharma, H.; Sastry, G. N. Frontiers in Chemistry, 2021, 9, 738852.
doi
[26]
Study of Lipid Heterogeneity on Bilayer Membranes Using Molecular Dynamics Simulations
Kumar, N.; Sastry, G. N. J. Mol. Graph. Model., 2021, 108, 108000.
doi
[27]
A Perspective on the Nature of Cation-π Interactions
Kumar, N.; Gaur, A. S.; Sastry, G. N. J. Chem. Sci., 2021, 133, 97.
doi
[28]
Assessing Therapeutic Potential of Molecules: Molecular Property Diagnostic Suite for Tuberculosis
Gaur, A. S.; […]; Kumar, N.; […]; Sastry, G. N. J. Chem. Sci., 2017, 129, 515.
doi

Book chapters

[1]
Advances in Bioactive Peptide Discovery: From Machine Learning to Protein Language Models
Kumar, N.; Li, Y. (2025). In: G. Narahari Sastry, H. J. Mahanta, N. Selvaraman, & T. C. Dinadayalane (eds.), Metamorphosis in Computational Chemistry Driven by Artificial Intelligence and Industry 5.0. Elsevier. (Submitted)
[2]
Chemical Processing – Wet Extraction and Improvement Strategies
Kumar, N.; Rajpurohit, B.; Li, Y. (2025). In: F. Boukid, M. C. Tulbek, S. Ganeshan, & Y. Wang (eds.), Pulse Breeding, Processing, Functionality, and Products, Elsevier. (Accepted)
[3]
Predicting Peptide Bioactivity Using the Unified Model Architecture UniDL4BioPep
Du, Z.; Kumar, N.; Li, Y. (2025). In: KC, D. B. (Ed.), Large Language Models (LLMs) in Protein Bioinformatics. Springer US, New York, NY, pp. 279–292.
doi
[4]
Applications of Molecular Dynamics Simulation and MM-PBSA Methods in Discovery of Veterinary Drugs
Kumar, N.; Mandal, P.; Kumar, B.; Rani, P.; Singh, D. V. (2025). In: Kim, J.-M.; Pathak, R. K. (Eds.), Bioinformatics in Veterinary Science: Vetinformatics. Springer Nature, Singapore, pp. 325–366.
doi
[5]
Chapter 9 – Protein Chemistry, Structure, Synthesis, and Functional Properties
Bean, S. R.; Ioerger, B. P.; Tilley, M.; […]; Kumar, N.; Li, Y. (2025). In: Taylor, J. R. N.; Bean, S. R.; Duodu, K. G. (Eds.), Sorghum and Millets, 3rd ed., Elsevier, pp. 233–269.
doi
[6]
Overview of Plant-Based Proteins
Du, Z.; Rajpurohit, B.; Kumar, N.; Li, Y. (2025). In: Li, Y. (Ed.), Plant-Based Proteins: Production, Physicochemical, Functional, and Sensory Properties. Springer US, New York, NY, pp. 3–19.
doi
[7]
Free Amino and Sulfhydryl Group Content
Xiao, R.; Hu, R.; Kumar, N.; Li, Y. (2025). In: Li, Y. (Ed.), Plant-Based Proteins: Production, Physicochemical, Functional, and Sensory Properties. Springer US, New York, NY, pp. 123–132.
doi

Patent

[1]
6-Ethoxy-4-N-(2-Morpholin-4-Ylethyl)-2-N-Propan-2-yl-1,3,5-Triazine-2,4-Diamine Endowed with Herbicidal Activity Against Susceptible and Resistant Biotypes of Phalaris minor
Patent Application Publication No.: 202031045338 A. Application Filing Date: 18/10/2020. Publication Date: 04/12/2020. Inventors: Durg Vijay Singh, Priyanka Rani, Nandan Kumar, Shikha Agarwal. Assignee: Central University of South Bihar, Gaya, India.
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