Research & Projects | Dheeraj Kumar Chaurasia

Core Competencies

MD Simulations

Extensive experience using the AMBER software suite for simulating protein-ligand dynamics. Analyzing trajectories using cpptraj to calculate RMSD, RMSF, and Hydrogen Bonds to understand stability.

Machine Learning

Developing ensemble models (XGBoost, Random Forest) to predict binding affinities. Expert in dataset curation from PDBbind and feature extraction for QSAR modeling.

Tool Development

Full-stack implementation of scientific tools. I bridge the gap between Python backend logic and user-friendly Web interfaces (PHP/JS) hosted on Linux HPC clusters.

Featured Projects

SEARCH-ML Framework

Virtual Screening Tool

A comprehensive scoring function developed to improve the accuracy of protein-ligand binding affinity predictions. Trained on a curated dataset of 11,689 complexes from PDBbind, this tool utilizes an ensemble of machine learning algorithms to outperform classical scoring functions.

Python Scikit-Learn Bash Scripting HPC

Read Documentation

ProteoLig-ML

Target Identification

An ongoing initiative to map protein-ligand interactions across specific viral targets. This project integrates molecular docking pipelines with machine learning refinement stages to filter false positives in high-throughput screening campaigns.

Bioinformatics Docking Web Dev

Publications & Manuscripts

2026

Manuscript Submitted

Stack-Tox: A data driven small molecule toxicity predictor

Toxicological Sciences (Manuscript Submitted)

Shireen Shaikh, Haryaksh Bhardwaj, Tarun Warrier, Dheeraj Kumar Chaurasia, Shashank Shekhar, Ashwin Srinivasan, B Jayaram, and Raviprasad Aduri

2026

Manuscript Submitted

SEARCH-ML: A Stacked Ensemble QSAR Framework for Efficient Protein-Ligand Binding Affinity Prediction

Journal of Computational Chemistry (Manuscript Submitted)

Dheeraj Kumar Chaurasia, Madhvi Mishra, Aman Sharma, B. Jayaram, et al.

2026

Published

Sanjeevini 3.0: An enhanced comprehensive automated web server for Computer-Aided Drug Design.

Medinformatics, Bon View Publishing (Manuscript Submitted)

Dheeraj Kumar Chaurasia, Aman Sharma, Madhvi Mishra, Akanksha Kesarwani, Raushan Anjum, Shashank Shekhar, Aditya Mittal, and B. Jayaram

View Article

2026

Published

Machine learning augmented rapid screening and scoring for an effective search for lead molecules in computer aided drug discovery

RSC Book Chapter

B Jayaram, Dheeraj Kumar Chaurasia, and Pradeep Pant

View Article

2026

Published

In-silico evaluation of Hedychium spicatum phytochemicals as potential COX-2 inhibitors: molecular docking, dynamics simulation, and ADMET analysis

In Silico Pharmacology

Manju Singh, Aman Sharma, Dheeraj Kumar Chaurasia, et al.

View Article

2026

Published

BIMP: Unveiling the Phytochemical Richness of Indian Medicinal Plants as Potential Therapeutic Agents

Global Trends in Health, Technology and Management II

Dheeraj Kumar Chaurasia, Raushan Anjum, Aman Sharma, et al.

View Article

2026

Published

Prioritising Candidate Drugs via Virtual Screening, Molecular Docking, and MD Simulations

Springer Handbook of Chem- and Bioinformatics

Dheeraj Kumar Chaurasia, Raushan Anjum, Dr. Ashutosh Shandilya, et al.

View Article

2025

Published

BgDB: a comprehensive genomic resource information system of bitter gourd for accelerated breeding programme

Database (Oxford Academic)

P Saini, A Singh, T Chandra, D.K. Chaurasia, et al.

View Article

2025

Published

Exploring chemical space for “druglike” small molecules in the age of AI

Frontiers in Molecular Biosciences

AA Kattuparambil, D.K. Chaurasia, S Shekhar, et al.

View Article

2023

Published

Mining of molecular insights of CYP2A6 and its variants complex with coumarin using MD simulation

Journal of Biomolecular Structure and Dynamics

A Yadav, A Kesharwani, D.K. Chaurasia, P Katara

View Article

2022

Published

Repurposing of FDA approved drugs and their validation against potential drug targets for Salmonella enterica

Journal of Biomolecular Structure and Dynamics

A Kesharwani, D.K. Chaurasia, P Katara

View Article

2021

Published

Molecular Simulation–Driven Drug Repurposing for the Identification of Inhibitors Against Non-Structural Proteins of SARS-CoV-2

In Silico Modeling of Drugs Against Coronaviruses

A Pathak, B Singh, D.K. Chaurasia, B Jayaram

View Article

2021

Published

Virtual screening, ADMET prediction and dynamics simulation of potential compounds targeting the main protease of SARS-CoV-2

Journal of Biomolecular Structure and Dynamics

R Yadav, M Imran, P Dhamija, D.K. Chaurasia, S Handu

View Article

2020

Published

PvP01-DB: computational structural and functional characterization of soluble proteome of PvP01 strain of Plasmodium vivax

Database (Oxford)

A Singh, R Kaushik, D.K. Chaurasia, M Singh, B Jayaram

View Article