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yboulaamane/README.md

Hi, I'm Yassir Boulaamane 👋

Postdoctoral Researcher at InSiliChem, Universitat Autònoma de Barcelona
PhD in Computational Drug Discovery · AI and physics-based molecular modelling

  • Now: predicting P450 metabolism, and building open tools for computational drug discovery (BioLatent, Assayer).
  • Research interests: natural products, neurodegenerative diseases and antimicrobial resistance.
  • Learning: free energy perturbation and umbrella sampling.
  • Open to collaborations on in silico drug design, QSAR, docking and molecular dynamics. Email me.

Website ORCID Google Scholar LinkedIn ResearchGate X Email

Featured projects

Assayer · assayer.vercel.app
A catalogue of 2,000+ medicinal and computational chemistry tools (300 curated by hand), plus step-by-step protocols that say which tools to use at each step and what it has to prove before you move on.

BioLatent · biolatent.vercel.app
A registry and benchmark of molecular, protein and nucleic-acid representations. Version 1.1.0 compares 18 frozen representations across 9 tasks under one prespecified protocol.

Sorbent
A compound triage service built on FastAPI and RDKit. Submit a SMILES library, get back a ranked, deduplicated, liability-flagged shortlist where every number is deterministic and citable.

Learn CADD · learn-cadd.vercel.app
An interactive, first-principles course on computer-aided drug design: 18 modules, each pairing theory with a browser playground.

Awesome Drug Discovery Stars
A curated resource list on computational methods for drug discovery.

More projects

  • QSARBoost: a Python framework for building, validating and applying gradient boosting QSAR models.
  • QSARBioPred: a Jupyter notebook for building QSAR classification models for bioactivity prediction.
  • EnsembleBBB: an ensemble machine learning model for predicting blood-brain barrier permeability.
  • VinaScreen: an automated AutoDock Vina script for structure-based virtual screening.
  • GMXPlotter: a reproducible analysis workflow for GROMACS MD simulations on Google Colab.
  • CoumarinDB and ArtemisiaDB: curated databases of naturally occurring coumarins and of secondary metabolites from Artemisia species.
  • comp_chem_colab: Jupyter notebooks for computational chemists.

Tools I work with

Cheminformatics and ML: Python, RDKit, scikit-learn, PyTorch, Hugging Face Transformers
Simulation and docking: GROMACS, AutoDock Vina
Software: FastAPI, Next.js, TypeScript, Jupyter, Linux, Bash

Publications

Recent papers are listed on my website and Google Scholar.

Pinned Loading

  1. awesome-drug-discovery awesome-drug-discovery Public

    A meticulously curated resource list focused on computational methods for drug discovery.

    158 49

  2. QSARBioPred QSARBioPred Public

    A Jupyter Notebook to build QSAR classification models for bioactivity prediction.

    Jupyter Notebook 7 3

  3. CoumarinDB CoumarinDB Public

    A manually curated database containing chemical information for naturally occurring coumarins.

    JavaScript 1

  4. BBBScope BBBScope Public

    Blood-brain barrier permeability prediction that reports how far each compound sits from the training data, and what that costs in accuracy.

    Python 1

  5. VinaScreen VinaScreen Public

    An automated Vina script for structure-based virtual screening

    Python 1

  6. ArtemisiaDB ArtemisiaDB Public

    A curated database containing chemical information of secondary metabolites isolated from Artemesia L. species.

    JavaScript 1