Publications
My work spans protein language models and AI-guided peptide prediction, molecular simulations and membrane biophysics, food protein structure–function modeling, non-covalent interaction chemistry, and computational drug discovery platforms. Below is a curated list of manuscripts, peer-reviewed journal articles, book chapters, databases, and intellectual property contributions.
Citation metrics: Citations 400+ · h-index 11 · i10-index 11. A live list is available on Google Scholar .
25+
Peer-reviewed
articles
articles
7+
Submitted /
in preparation
in preparation
8+
Book
chapters
chapters
1
Patent
Selected highlights
Cover
AI / ML
pLM4CPPs: Protein Language Model-Based Predictor for Cell Penetrating Peptides
Introduced a protein language model-based deep learning framework for predicting cell-penetrating peptides.
Cover
Membranes
Membrane Selectivity Mechanisms of the Antimicrobial Peptide Snakin-Z Against Prokaryotic and Eukaryotic Membrane Models
Provided atomistic insight into how antimicrobial peptides discriminate between bacterial and mammalian membrane models.
Cover
Food proteins
Solvent-Dependent Structural and Dynamic Behavior of α-Gliadin in Aqueous Ethanol Systems: Insights from Molecular Dynamics Simulations
Used molecular simulations to connect ethanol-water environments with α-gliadin structural dynamics and aggregation-relevant behavior.
Cover
Non-covalent
Towards Developing a Criterion to Characterize Non-Covalent Bonds
Developed quantum mechanical insight into the characterization and interpretation of non-covalent bonding.
Cover
Databases
Analyzing the Aromatic–Aromatic Interactions in Proteins: A2ID 2.0
Contributed to a protein interaction database supporting systematic analysis of aromatic–aromatic interactions.
Cover
Review
Comprehensive Review of Chickpea (Cicer arietinum): Nutritional Significance, Health Benefits, Techno-functionalities, and Food Applications
Synthesized current knowledge on chickpea nutrition, functionality, health relevance, and food applications.
Journal covers
Selected journal covers and representative publication venues highlighting research contributions in protein language models, molecular simulations, membrane biophysics, food protein science, computational chemistry, and AI-driven molecular discovery. Clicking a cover redirects to the corresponding journal or publication page.
JCIM
J. Chem. Inf. Model.
pLM4CPPs for cell penetrating peptides
MMB
Methods in Molecular Biology
UniDL4BioPep for bioactive peptide predictions
JPCB
J. Phys. Chem. B
Selectivity of Snakin-Z against microbial membranes
PROT
Proteins
Database for mining cation-aromatic interactions in proteins
FC
Food Chemistry
Multiscale modeling of α-Gliadin, Ovalbumin proteins · NIR-ML
PCCP
Phys. Chem. Chem. Phys.
Development of parameters for non-covalent intteractions
IJBM
Int. J. Biol. Macromol.
Database for mining aromatic-aromatic interactions in proteins · modeling of myofibrillar protein
JCS
J Chem Sci
perspective on the nature of cation-π interactions, development of MPDS-TB
JMM
J Mol Model
Modeling and simulation for herbicide discovery
MD
Molecular Diversity
Development of MPDS modules such as compound and fragment library
JMGM
J. Mol. Graph. Model.
Lipid heterogeneity simulations
JBSD
J. Biomol. Struct. Dyn.
Drug repurposing
GS
Gigabyte
Molecular Property Diagnostic Suite for COVID-19
MDVD
Methods and Protocols in Food Science
MD simulations for veterinary drugs
CRFSFS
Compr. Rev. Food Sci. Food Saf.
Chickpea review
FRI
Food Research International
Ovalbumin allergenicity
MPFC
Methods and Protocols in Food Science
Free amino and sulfhydryl group content
Foods
Foods
Frozen dough cryoprotection
CTN
Sorghum and Millets
Protein chemistry, structure and functional properties
WMB
World J Microbiol Biotechnol
DFT for Characterizing arsenic tolerance
TCA
Theor Chem Acc
Solvation of metal ions
JCC
J Comput Chem
Binding propensity and selectivity of ions
Frontiers
Frontiers in Chemistry
Metal ion water interactions
RSC
RSC Advances
Charactrization of covalent and non-covalent interactionsSelected highly cited works
HC
Towards Developing a Criterion to Characterize Non-Covalent Bonds: A Quantum Mechanical Study
A major contribution to quantum mechanical interpretation of non-covalent bond characterization.
HC
A Perspective on the Nature of Cation-π Interactions
Summarized mechanistic and energetic features of cation–π interactions relevant to biomolecular recognition.
HC
Comprehensive Review of Chickpea: Nutritional Significance, Health Benefits, Functionalities, and Food Applications
A broad review covering nutritional, functional, and food application aspects of chickpea.
HC
Study of Lipid Heterogeneity on Bilayer Membranes Using Molecular Dynamics Simulations
Demonstrated molecular simulation-based analysis of lipid heterogeneity and membrane organization.
Peer-reviewed journal articles
Solvent-Dependent Structural and Dynamic Behavior of α-Gliadin in Aqueous Ethanol Systems: Insights from Molecular Dynamics Simulations
Ferrichrysin Siderophore from Gangetic Aspergillus japonicus: Isolation, Characterization, and Role in Sustained Arsenic Tolerance
Modification of Structural Properties and Potential Allergenicity of Ovalbumin Induced by Ultrasound Treatment During in vitro Digestion
Membrane Selectivity Mechanisms of Antimicrobial Peptide Snakin-Z against Prokaryotic and Eukaryotic Membrane Models
pLM4CPPs: Protein Language Model-Based Predictor for Cell Penetrating Peptides
Comprehensive Review of Chickpea (Cicer arietinum): Nutritional Significance, Health Benefits, Functionalities, and Food Applications
Changes of Digestive Stability and Potential Allergenicity of High Hydrostatic Pressure-Treated Ovalbumin During in vitro Digestion
Changes of Structure Properties and Potential Allergenicity of Ovalbumin under High Hydrostatic Pressures
Pea Protein-Stabilized Emulsion as a High-Performance Cryoprotectant in Frozen Dough: Effects on the Storage Stability and Baking Performance
Co-Stabilization Effects of Gluten/Carrageenan to the Over-Heated Myofibrillar Protein: Inhibit the Undesirable Gel Weakening and Protein Over-Aggregations
Molecular Property Diagnostic Suite for COVID-19 (MPDS COVID-19): An Open Access Disease-Specific Drug Discovery Portal
Analyzing the Aromatic–Aromatic Interactions in Proteins: A2ID 2.0
Analyzing the Cation–Aromatic Interactions in Proteins: Cation-Aromatic Database V2.0
Molecular Property Diagnostic Suite Compound Library (MPDS-CL): A Structure-Based Classification of the Chemical Space
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
First Principle Calculations on the Micro-Solvation of 3d-Transition Metal Ions: Solvation vs Splitting Water
Binding Propensity and Selectivity of Cationic, Anionic and Neutral Guests with Model Hydrophobic Hosts: A First Principles Study
Towards Systematic Exploration of Chemical Space: Building the Fragment Library Module in Molecular Property Diagnostic Suite
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
Repurposing of Approved Drugs to Predict New Inhibitors for Viral Infectious Diseases: A Molecular Modelling Approach
Towards Developing a Criterion to Characterize Non-Covalent Bonds: A Quantum Mechanical Study
Fate of Sc-Ion Interaction with Water: A Computational Study to Address Splitting Water Versus Solvating Sc Ion
Study of Lipid Heterogeneity on Bilayer Membranes Using Molecular Dynamics Simulations
A Perspective on the Nature of Cation-π Interactions
Assessing Therapeutic Potential of Molecules: Molecular Property Diagnostic Suite for Tuberculosis
Manuscripts submitted / under preparation
Molecular Mechanisms of Ice Recognition in Wild-Type and Disulfide-Stabilized FfIBP Variants: An All-Atom Molecular Dynamics Study
Focuses on atomistic mechanisms of ice recognition and structural stabilization in ice-binding protein variants.
Atomistic Insights into α-Gliadin Dimerization and Early Aggregation in Mixed Ethanol–Water Environments
Investigates early protein–protein association and aggregation behavior of α-gliadin in mixed solvent environments.
pLM4G-CPPs: Protein Language Model-Guided Graph Learning for Cell-Penetrating Peptides Prediction
Extends protein language model-based peptide prediction toward graph-based sequence and structure representation learning.
Concentration-Dependent Mechanisms of Melittin-Induced Pore Formation in Eukaryotic and Prokaryotic Membranes
Examines how peptide concentration regulates pore formation and membrane disruption across different membrane models.
Machine Learning-Driven NIR Spectroscopy for Rapid Prediction and Classification of Wheat Baking Quality
Applies machine learning to NIR spectroscopy for rapid wheat quality prediction and classification.
All-Atom to Coarse-Grained Simulations of Food Proteins: Principles, Force Fields, and Applications
Reviews simulation strategies connecting all-atom and coarse-grained models for food protein applications.
Charge-Mediated Cryoprotective Behaviors of Oligosaccharides to Myosin Denaturation: Molecular Insights from Protein-Saccharide Interactions
Explores molecular mechanisms of protein–saccharide interactions underlying cryoprotection.
Book chapters
Artificial Intelligence (AI)-Driven Optimization of Enzymatic Release of Bioactive Peptides
Advances in Bioactive Peptide Discovery: From Machine Learning to Protein Language Models
Chemical Processing – Wet Extraction and Improvement Strategies
Predicting Peptide Bioactivity Using the Unified Model Architecture UniDL4BioPep
Applications of Molecular Dynamics Simulation and MM-PBSA Methods in Discovery of Veterinary Drugs
Chapter 9 – Protein Chemistry, Structure, Synthesis, and Functional Properties
Overview of Plant-Based Proteins
Free Amino and Sulfhydryl Group Content
Patent
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