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mondalsou/README.md

Hi, I'm Sourav Mondal, PhD 👋

AI/ML Scientist | Computational Chemist | Drug Discovery

PortfolioLinkedInGitHubEmail


🧬 About Me

Computational scientist with 10+ years of experience in cross-disciplinary research spanning Drug Discovery and Materials Modeling. Currently at Aganitha Cognitive Solutions, leveraging quantum mechanical calculations and deep learning to accelerate small molecule research.

  • 🔬 Building end-to-end pipelines for crystal structure prediction, conformer generation, pKa estimation, and ADMET property calculations
  • 📚 Published in Nature Computational Materials, JACS, and Nano Letters
  • 🎓 PhD from JNCASR Bangalore | Postdoc at Trinity College Dublin

🔭 Current Work at Aganitha Cognitive Solutions

ProjectDescription
Crystal Structure PredictionGraph Neural Networks for rapid polymorph screening of drug-like molecules
Conformer GenerationAI-driven platform enabling environment-aware conformer generation for advanced drug discovery applications
pKa EstimationTwo complementary modeling approaches—QM-based and GNN-based—for pKa estimation under non-aqueous conditions
ADMET PredictionPhysics-based QM platform for high-accuracy prediction of key thermodynamic properties: solubility, logP, and solvation energy

🚀 Featured Projects

ProjectStackHighlights
Drug Discovery TriageReact · FastAPI · RDKitReal-time ADMET predictions, QED scoring, PAINS alerts, live demo
Solubility Dual-Graph GNNPyTorch · MPNN · Cross-AttentionR²=0.90 on 100K+ solute-solvent pairs (BigSolDB 2.0)
Lead Optimization AgentLangChain · RDKit · StreamlitAI agent loop for iterative structural optimization with property tracking
GNN Bind OptimizerPyTorch · PyG · REINFORCE · MLflowHeterogeneous GNN for binding affinity + RL-based pocket-conditioned molecule generation
Formulation Bayesian OptimizationBoTorch · GPyTorch · RDKit · StreamlitBayesian optimization pipeline for pharmaceutical formulation design — multi-objective GP surrogate with acquisition function tuning

🛠️ Technical Skills

AI/ML & Deep Learning

Gen AIPyTorchTensorFlowGNNTransformersAI AgentsLangChainBayesian OptimizationBoTorchScikit-learnReinforcement LearningTransfer LearningMulti-task LearningLSTM

Computational Chemistry

CP2KORCApsi-4PySCFDFT/SAPTML Force Fields

Cheminformatics

RDKitASESMILESADMETDockingCADDBinding AffinityLead Optimization

Programming & Tools

PythonFortranDockerAzureGitn8nStreamlitSQL ServerMLflow


📚 Featured Publications

YearPublicationJournal
2025The spin phonon relaxation of single molecules magnet in the presence of strong exchange couplingACS Cent. Sci.
2023Spin-phonon decoherence in solid-state paramagnetic defects from first principlesnpj Comput. Mat.
2022Unravelling the contributions to spin-lattice relaxation in Kramers single-molecule magnetsJ. Am. Chem. Soc.
2022Identification and Manipulation of Defects in Black PhosphorusJ. Phys. Chem. Lett.
2020Direct Observation of the Reduction of a Molecule on a Nitrogen pair in Doped GrapheneNano Lett.

📊 GitHub Stats

GitHub Stats

Top Languages


🎓 Education

  • PhD in Computational Material Science - JNCASR, Bangalore (2015-2020)
  • M.Sc in Chemistry - IIT Guwahati (2012-2014)

📫 Let's Connect

📍 Hyderabad, India | 📧 souravchembwn@gmail.com | 📱 +91 9740851654

PortfolioCV


Computational Scientist | AI/ML Engineer | Building intelligent systems at the intersection of science and technology

Pinned Loading

  1. solubility-dual-graph-gnnsolubility-dual-graph-gnnPublic

    Dual-graph interaction GNN for predicting molecular solubility (logS) from solute-solvent SMILES using cross-attention and BigSolDB 2.0

    Jupyter Notebook

  2. lead-optimization-agentlead-optimization-agentPublic

    AI agent (LangChain + RDKit + Streamlit) for iterative lead optimization — proposes structural changes, scores ADMET/QED/BBB properties, and tracks the candidate journey visually

    Python

  3. gnn-bind-optimizergnn-bind-optimizerPublic

    Heterogeneous GNN for protein-ligand binding affinity prediction + REINFORCE molecular generator · EGFR kinase · SQL Server · MLflow · Streamlit

    Jupyter Notebook

  4. quantum-pharma-labquantum-pharma-labPublic

    Quantum pharma demo using QAOA and Qiskit to select drug candidates from molecular datasets, with classical ML baselines and an interactive wave-interference explainer.

    Jupyter Notebook

  5. formulation-bayesian-optimizationformulation-bayesian-optimizationPublic

    Model-based DoE and Bayesian optimization for pharmaceutical formulation: GP-guided Q45 optimization with EI/LogEI, plus qNEHVI multi-objective trade-offs (Q45, hardness, friability).

    Jupyter Notebook

  6. regdociqregdociqPublic

    Minimal PDF RAG demo: BM25 retrieval + LLM via OpenRouter. Upload any PDF, ask questions, get cited answers. No vector DB needed.

    Jupyter Notebook