Curriculum vitae

Work experience

2020 - now: Research Assistant - Organic Chemistry Department

Methodology development
- MolUtil: molecular standardization, featurization, medicinal chemistry filtration, and chemical space visualization (incorporate with RDKit)
- DockValid: automated result extraction and validation (retrospective control-ROC plot)
Application of AI methods in drug discovery
- HIV-1 integrase (Master thesis): QSAR pipeline for data type selection and model building, pharmacophore modeling with ensemble methods, alphafold2 for protein curation and benchmarking molecular docking packages (Vina, Smina, Qvina2, Vina GPU, Autodock GPU)
Supervisor: Assoc.Prof.Truong Ngoc Tuyen, PhD

Skills

Programming: Python, C++, Linux, Git, OOP

Cheminformatics: RDKit, Openbabel, deepchem, chemprop

Protein Modelling: Pymol, Autodock, Gromacs, VMD, MDAnalysis, MDTraj, MOE

Data science

Data analysis: visualization (seaborn, matplotlib, plotly), linear algebra, calculus, probability and statistics (numpy, pandas)
Data mining: data pipeline development including handle low variance features, missing values, univariate and multivariate outliers; conduct statistical test for decision making in model selection using cross-validation
Machine learning: scikit-learn, imblearn, XGBoost, CatBoost, optimization (grid search and bayesian search)
Deep Learning: Pytorch, Tensorflow, Keras, CNNs, RNNs, GNN.

Process Automation: Molecular docking pipeline automation, Molecular dynamics automation

Personal skill: Problem solving, crictical thinking, communication

Publications

Synthesis of monocarbonyl analogues of curcumin containing 1-(4-nitrophenyl)-1H-pyrazole and 1,3-diphenyl-1H-pyrazole heterocyclics

Thi Khanh Ngan Nguyen, Quoc Hoai Nam Đoan, Bao Ngoc Nguyen, Thanh An Pham, Tran Anh Thu Vu, Anh Tien Le, Ngoc Tuyen Truong. Synthesis of monocarbonyl analogues of curcumin containing 1-(4-nitrophenyl)-1H-pyrazole and 1,3-diphenyl-1H-pyrazole heterocyclics. Vietnamese Pharmacy Journal (Accepted).

Study on the effect of molecular fingerprints on the performance of machine learning model predicting hiv integrase bioactivty

Tieu Long Phan, Thanh An Pham, Bao Vy Doan Ngoc, Hoang Son Le Lai, Ngoc Tuyen Truong (2023). Study on the effect of molecular fingerprints on the performance of machine learning model predicting HIV integrase bioactivty. Vietnamese Pharmacy Journal (Accepted).

Thanh-An Pham

Curriculum vitae

Education

Work experience

Skills

Language

Course

Publications

Synthesis of monocarbonyl analogues of curcumin containing 1-(4-nitrophenyl)-1H-pyrazole and 1,3-diphenyl-1H-pyrazole heterocyclics

Study on the effect of molecular fingerprints on the performance of machine learning model predicting hiv integrase bioactivty

Honours

References