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@coleygroup Coley Research Group @ MIT

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    Repositories list

    47 repositories

    • PolymerLit

      Public
      The data repo for polymer image recognition
      Python
      •
      MIT License
      •0•2•0•0•Updated Oct 19, 2026Oct 19, 2026

    • coleygroup.github.io

      Public
      Coley Research Group website
      SCSS
      •44•5•3•1•Updated Oct 18, 2026Oct 18, 2026

    • MIST

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 11, 2026Oct 11, 2026

    • coley-opentrons

      Public
      For uploading scripts to the Opentrons
      0•0•0•0•Updated Oct 9, 2026Oct 9, 2026

    • msms-structure-elucidation.skills

      Public
      Skills for MS/MS-based small molecule structural elucidation for Codex, Claude Code, and more.
      Python
      •
      MIT License
      •0•3•1•0•Updated Oct 9, 2026Oct 9, 2026

    • foam

      Public
      de novo structural elucidation from mass spectra with forward spectrum simulation models
      Python
      •
      MIT License
      •3•6•0•0•Updated Oct 7, 2026Oct 7, 2026

    • Audit_ML_MS_analysis

      Public
      Audit and reanalysis of fingerprint prediction models for small-molecule mass spectrometry
      Python
      •
      MIT License
      •2•0•0•0•Updated Oct 5, 2026Oct 5, 2026

    • ms-pred

      Public
      Predicting tandem mass spectra from molecules
      Jupyter Notebook
      •
      MIT License
      •42•168•4•0•Updated Oct 5, 2026Oct 5, 2026

    • notes-1034

      Public
      Jupyter Notebook
      •
      Other
      •1•1•1•0•Updated Sep 30, 2026Sep 30, 2026

    • icicle

      Public
      Fragment-Grounded Neural Simulation of EI-MS Spectra for Structure Elucidation at Library Scale
      Python
      •
      MIT License
      •1•4•0•0•Updated Sep 21, 2026Sep 21, 2026

    • shepherd2

      Public
      ShEPhERD-2 code: Interaction Profiles as a Universal Language for Generative Molecular Design
      drug-discoverydrug-designgenerative-ai
      drug-discoverydrug-designgenerative-ai
      Python
      •
      MIT License
      •10•61•1•1•Updated Sep 16, 2026Sep 16, 2026

    • shepherd-score

      Public
      Interaction profile extraction, scoring, alignment and evaluation of ShEPhERD. [ICLR 2025]
      Python
      •
      MIT License
      •11•41•0•0•Updated Sep 8, 2026Sep 8, 2026

    • FRIGID

      Public
      Scaling diffusion-based molecular generation from mass spectra at training and inference time
      Python
      •5•25•5•1•Updated Aug 20, 2026Aug 20, 2026

    • scale-up-llm-extraction

      Public
      for the manuscript, "Automated Extraction and Evaluation of Process Chemistry Scale-Up Insights"
      Jupyter Notebook
      •0•0•0•0•Updated Jul 13, 2026Jul 13, 2026

    • ML4MolEng

      Public
      Materials for the course Machine Learning for Molecular Engineering (3/7/10/20.C01/C51)
      Jupyter Notebook
      •8•33•0•0•Updated May 14, 2026May 14, 2026

    • rdkit

      Public
      The official sources for the RDKit library
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •1.1k•0•0•0•Updated Apr 30, 2026Apr 30, 2026

    • shepherd

      Public
      Training and inference code for ShEPhERD: Diffusing shape, electrostatics, and pharmacophores for bioisosteric drug design [ICLR 2025 oral]
      drug-discoverydrug-designgenerative-ai
      drug-discoverydrug-designgenerative-ai
      Python
      •
      MIT License
      •13•97•7•0•Updated Mar 31, 2026Mar 31, 2026

    • DiffMS

      Public
      Python
      •
      MIT License
      •30•125•8•0•Updated Mar 10, 2026Mar 10, 2026

    • cluster-status

      Public
      Python
      •1•0•0•0•Updated Mar 3, 2026Mar 3, 2026

    • rdcanon

      Public
      SMARTS sanitization
      Jupyter Notebook
      •
      MIT License
      •5•34•0•0•Updated Mar 2, 2026Mar 2, 2026

    • virtual_flask

      Public
      Software associated with Automated Invention of MCRs paper
      Jupyter Notebook
      •
      MIT License
      •1•9•0•0•Updated Feb 13, 2026Feb 13, 2026

    • quarc

      Public
      Python
      •
      MIT License
      •2•17•0•0•Updated Oct 1, 2025Oct 1, 2025

    • pyscreener

      Public
      pythonic interface to virtual screening software
      distributed-computingcomputational-biologyray
      distributed-computingcomputational-biologyrayvirtual-screeningmolecular-docking
      Python
      •
      MIT License
      •34•95•2•4•Updated Sep 4, 2025Sep 4, 2025

    • sparrow

      Public
      Jupyter Notebook
      •
      MIT License
      •6•64•0•0•Updated Jun 30, 2025Jun 30, 2025

    • ml-for-tb

      Public
      surrogate models for TB inhibitors
      Jupyter Notebook
      •1•1•0•0•Updated Feb 4, 2025Feb 4, 2025

    • desp

      Public
      Double-Ended Synthesis Planning with Goal-Constrained Bidirectional Search (NeurIPS 2024)
      Python
      •
      MIT License
      •7•31•2•1•Updated Jan 23, 2025Jan 23, 2025

    • molpal

      Public
      active learning for accelerated high-throughput virtual screening
      chemistryactive-learningvirtual-screening
      chemistryactive-learningvirtual-screening
      Jupyter Notebook
      •
      MIT License
      •45•215•10•1•Updated Jun 15, 2024Jun 15, 2024

    • aspire_epv

      Public
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Jun 3, 2024Jun 3, 2024

    • variational-reaction-center

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 6, 2024Feb 6, 2024

    • bio_orthogonal_click_reactions

      Public
      The code and data associated to the project on screening for new bio-orthogonal click reactions
      Python
      •
      MIT License
      •1•8•0•0•Updated Jan 10, 2024Jan 10, 2024
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