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    47 repositories

    • 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
      •6•35•3•0•Updated Sep 16, 2025Sep 16, 2025

    • pdzext

      Public
      Allosteric and Energetic Remodeling by Protein Domain Extensions
      R
      •
      MIT License
      •0•0•0•0•Updated Aug 1, 2025Aug 1, 2025

    • PDZ_homologs

      Public
      HTML
      •
      MIT License
      •0•0•0•0•Updated Jul 22, 2025Jul 22, 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 Science 2025
      Jupyter Notebook
      •0•1•0•0•Updated Jul 21, 2025Jul 21, 2025

    • allostery_pathogenicity

      Public
      R
      •
      MIT License
      •0•1•0•0•Updated Jul 11, 2025Jul 11, 2025

    • ABA_receptor

      Public
      Companion scripts for DMS data processing, dose-response curve fitting and figure reproduction ("The genetic architecture of an allosteric hormone receptor", Stammnitz & Lehner, biorXiv 2025)
      protein-structureplantsallosteryprotein-protein-interactionreceptorprotein-ligand-interactionsgenomics-visualizationhormonesgenomics-data
      R
      •1•1•0•0•Updated Jul 4, 2025Jul 4, 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 Mighell and Ben Lehner
      Jupyter Notebook
      •0•1•0•0•Updated Jun 2, 2025Jun 2, 2025

    • canya

      Public
      A hybrid neural network to predict nucleation propensity
      Python
      •
      MIT License
      •2•7•0•0•Updated May 7, 2025May 7, 2025

    • MoCHI

      Public
      Neural networks to fit interpretable models and quantify energies, energetic couplings, epistasis, and allostery from deep mutational scanning data
      Python
      •
      MIT License
      •5•53•0•0•Updated Apr 10, 2025Apr 10, 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•0•0•0•Updated Dec 19, 2024Dec 19, 2024

    • domainome

      Public
      MIT License
      •0•15•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, energetic couplings, epistasis and allostery from deep mutational scanning data (Faure AJ & Lehner B, 2024)
      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•3•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 readthrough of pathogenic premature termination codons (Toledano I, Supek F & Lehner B, 2023)
      MIT License
      •0•3•0•0•Updated Jul 13, 2024Jul 13, 2024

    • fuzzy_specificity

      Public
      Code for "A complete map of specificity encoding for a partially fuzzy protein interaction" by Taraneh Zarin and Ben Lehner
      R
      •
      MIT License
      •0•0•0•0•Updated Apr 26, 2024Apr 26, 2024

    • deep_indel_mutagenesis

      Public
      R
      •
      MIT License
      •1•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 epistasis in genetic landscapes of arbitrary shape and complexity (Faure AJ, et al., 2023)
      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 (Weng C, Faure AJ & Lehner B, 2022)
      R
      •
      MIT License
      •0•4•0•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 allosteric landscapes of protein binding domains (Faure AJ, Domingo J & Schmiedel JM et al., 2022)
      R
      •
      MIT License
      •1•21•0•0•Updated Jul 20, 2023Jul 20, 2023

    • 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 allostery (Hidalgo-Carcedo C & Faure AJ et al., 2023)
      R
      •
      MIT License
      •0•0•0•0•Updated May 2, 2023May 2, 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: https://www.biorxiv.org/content/10.1101/2021.11.14.468508v1.
      R
      •
      MIT License
      •0•3•0•0•Updated May 15, 2022May 15, 2022

    • soma-germline-timing

      Public
      Scripts to analyze C. elegans soma and germline timings, to measure length of L1 larvae and to quantify embryo fluorescence as described in the paper 'Neuronal perception of the social environment generates an inherited memory that controls the development and generation time of C. elegans'
      R
      •0•1•0•0•Updated Aug 3, 2021Aug 3, 2021

    • Higher-order_epistasis_tRNA

      Public
      Scripts needed to reproduce Domingo et al. 2018
      R
      •
      MIT License
      •1•3•0•0•Updated Oct 19, 2020Oct 19, 2020

    • Biophysical_Ambiguity

      Public
      Codes to reproduce the analysis and figures for the project "Biochemical ambiguities prevent accurate genetic prediction"
      R
      •
      MIT License
      •1•1•0•0•Updated Jul 13, 2020Jul 13, 2020

    • Constitutive_Exons

      Public
      Scripts needed to reproduce Baeza-Centurion et al. 2020
      R
      •1•2•0•0•Updated Jun 30, 2020Jun 30, 2020