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    51 repositories

    • Programmed_readthrough

      Public
      Programmed translational readthrough produces C-terminally extended protein isoforms via decoding of stop codons by near-cognate tRNAs. Here we use deep mutatio…
      R
      •
      MIT License
      •0•0•0•0•Updated Aug 31, 2026Aug 31, 2026

    • MoCHI

      Public
      Neural networks to fit interpretable models and quantify energies, energetic couplings, epistasis, and allostery from deep mutational scanning data
      Python
      •
      MIT License
      •11•57•2•1•Updated Aug 13, 2026Aug 13, 2026

    • allostery_pathogenicity

      Public
      Promela
      •
      MIT License
      •0•0•0•0•Updated Aug 10, 2026Aug 10, 2026

    • fuzzy_specificity

      Public
      Code for "A complete map of specificity encoding enables reprogramming of a protein interaction" by Taraneh Zarin, Cristina Hidalgo-Carcedo and Ben Lehner
      R
      •
      MIT License
      •0•2•0•0•Updated Aug 7, 2026Aug 7, 2026

    • phix174_WGM

      Public
      Complete mutagenesis of the genome and proteome of ΦX174
      Shell
      •0•0•0•0•Updated Aug 5, 2026Aug 5, 2026

    • OpenSplice

      Public
      This repository contains all code to reproduce the analyses and figures in the OpenSplice paper. OpenSplice quantifies the impact of >590,000 variants on the sp…
      Jupyter Notebook
      •
      MIT License
      •0•7•0•0•Updated May 27, 2026May 27, 2026

    • TF-MAPS

      Public
      TF-MAPS: fast high-resolution functional and allosteric mapping of DNA-binding proteins.
      R
      •
      MIT License
      •0•1•0•0•Updated May 11, 2026May 11, 2026

    • PDZ_homologs

      Public
      HTML
      •
      MIT License
      •0•2•0•0•Updated Feb 20, 2026Feb 20, 2026

    • pdzextms

      Public
      Source code for analyses and to reproduce all figures in the following publication: The effects of PDZ domain extensions on energies, energetic couplings and al…
      R
      •
      MIT License
      •0•0•0•0•Updated Jan 29, 2026Jan 29, 2026

    • pdzext

      Public
      Allosteric and Energetic Remodeling by Protein Domain Extensions
      R
      •
      MIT License
      •0•0•0•0•Updated Jan 28, 2026Jan 28, 2026

    • ABA_receptor

      Public
      Companion scripts for DMS data processing, dose-response curve fitting and figure reproduction ("The genetic architecture of an allosteric hormone receptor", St…
      protein-structureplantsallostery
      protein-structureplantsallosteryprotein-protein-interactionreceptorprotein-ligand-interactionsgenomics-visualizationhormonesgenomics-data
      R
      •2•1•0•0•Updated Nov 19, 2025Nov 19, 2025

    • src_allostery

      Public
      Source code for analyses and to reproduce all figures in the following publication: The allosteric landscape of Src (Beltran et al., 2023)
      MIT License
      •0•1•0•0•Updated Sep 20, 2025Sep 20, 2025

    • DiMSum

      Public
      An error model and pipeline for analyzing deep mutational scanning (DMS) data and diagnosing common experimental pathologies
      R
      •
      MIT License
      •8•45•4•0•Updated Sep 16, 2025Sep 16, 2025

    • combinatorialcores

      Public
      Source code for analyses and figure reproduction in "Genetics, energetics, and allostery in proteins with randomized cores and surfaces", Escobedo et. al Scienc…
      Jupyter Notebook
      •0•1•0•0•Updated Jul 21, 2025Jul 21, 2025

    • fas-indel-library

      Public
      R
      •0•0•0•0•Updated Jun 20, 2025Jun 20, 2025

    • GPCR-MAPS

      Public
      This repository contains the code to reproduce the analyses presented in the publication "The molecular basis of G-protein coupled receptor signaling" by Taylor…
      Jupyter Notebook
      •0•2•0•0•Updated Jun 2, 2025Jun 2, 2025

    • canya

      Public
      A hybrid neural network to predict nucleation propensity
      Python
      •
      MIT License
      •6•13•1•0•Updated May 7, 2025May 7, 2025

    • TECAN_analysis

      Public
      TECAN-reader based yeast growth measurements in R
      R
      •0•1•0•0•Updated Feb 28, 2025Feb 28, 2025

    • amyloids_energy_modelling

      Public
      Energetic modelling of Amyloid beta nucleation
      Jupyter Notebook
      •
      MIT License
      •1•1•0•0•Updated Feb 17, 2025Feb 17, 2025

    • V2R_surfexp_rescue

      Public
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Dec 19, 2024Dec 19, 2024

    • domainome

      Public
      MIT License
      •0•16•1•0•Updated Dec 10, 2024Dec 10, 2024

    • mochims

      Public
      Source code for analyses and to reproduce all figures in the following publication: MoCHI: neural networks to fit interpretable models and quantify energies, en…
      R
      •
      MIT License
      •0•0•0•0•Updated Aug 9, 2024Aug 9, 2024

    • archstabms

      Public
      Source code for analyses and to reproduce all figures in the following publication: The genetic architecture of protein stability (Faure AJ et al., 2024)
      R
      •
      MIT License
      •0•4•1•0•Updated Jul 28, 2024Jul 28, 2024

    • Stop_codon_readthrough

      Public
      Source code for computational analyses and to reproduce all figures in the following publication: Genome-scale quantification and prediction of drug-induced re…
      MIT License
      •0•4•0•0•Updated Jul 13, 2024Jul 13, 2024

    • deep_indel_mutagenesis

      Public
      R
      •
      MIT License
      •3•0•1•0•Updated Mar 19, 2024Mar 19, 2024

    • whmatrixextms

      Public
      Source code for analyses and to reproduce all figures in the following publication: An extension of the Walsh-Hadamard transform to calculate and model epistasi…
      Jupyter Notebook
      •
      MIT License
      •1•1•0•0•Updated Mar 8, 2024Mar 8, 2024

    • krasddpcams

      Public
      Source code for computational analyses and to reproduce all figures in the following publication: The energetic and allosteric landscape for KRAS inhibition (We…
      R
      •
      MIT License
      •0•4•2•0•Updated Nov 17, 2023Nov 17, 2023

    • doubledeepms

      Public
      Source code for fitting thermodynamic models (MoCHI), downstream analyses and to reproduce all figures in the following publication: Mapping the energetic and a…
      R
      •
      MIT License
      •1•22•0•0•Updated Jul 20, 2023Jul 20, 2023

    • SUNi_mutagenesis

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Feb 27, 2023Feb 27, 2023

    • RDGVassociation

      Public
      Script to (1) perform component extraction via ICA & VAE, (2) perform network analysis, and (3) replicate paper figures from manuscript. Pre-print on bioRxiv: h…
      R
      •
      MIT License
      •0•4•0•0•Updated May 15, 2022May 15, 2022
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