Repositories list

• multichains

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •11 fork•00 stars•00 issues•00 pull requests•Updated Apr 18, 2026Apr 18, 2026

• entanglement_misfolding_and_aging

  Public
  HTML

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 1, 2026Apr 1, 2026

• cg_simtk_protein_folding

  Public
  A toolkit for building CG model of protein/ribosome and MD simulation protocols for protein co- and post-translational folding

  simulation

  simulation

  Python

  •

  MIT License

  •11 fork•88 stars•00 issues•00 pull requests•Updated Dec 29, 2025Dec 29, 2025

• obrien-lab.github.io

  Public
  HTML

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 25, 2025Sep 25, 2025

• All_Atom_Misfolding_Exp_Ensemble

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •11 fork•00 stars•00 issues•00 pull requests•Updated May 4, 2025May 4, 2025

• IDP_NCLE

  Public
  Jupyter Notebook

  •11 fork•00 stars•00 issues•00 pull requests•Updated Apr 14, 2025Apr 14, 2025

• Properties-governing-native-state-entanglements-and-relationships-to-protein-function

  Public
  Python

  •

  MIT License

  •11 fork•00 stars•00 issues•00 pull requests•Updated Apr 9, 2025Apr 9, 2025

• Misfolded-ecPGK-structural-ensemble-consistent-with-LiP-MS-and-XL-MS-experiments

  Public
  This is a webapp for visualizing the misfolded structual ensemble of ecPGK that exhibit consistent structual changes identified in LiP-MS and XL-MS.

  JavaScript

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 20, 2025Mar 20, 2025

• visualize_entanglements

  Public
  This repository includes the interactive website (click the link below) that visualizes the example misfolded structures observed in our simulations that contai…

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 28, 2024Mar 28, 2024

• avoid-misfolding-into-non-covalent-lasso-entanglements-using-small-molecule-drugs

  Public
  Code and data for the paper "It is theoretically possible to avoid misfolding into non-covalent lasso entanglements using small molecule drugs"

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 28, 2023Dec 28, 2023

• aip_web_docker

  Public
  RiboA: Ribo-Seq A-site Identifier

  Python

  •

  MIT License

  •11 fork•11 star•00 issues•33 pull requests•Updated Apr 21, 2023Apr 21, 2023

• test_visual_LiPMS_consistency

  Public
  https://obrien-lab.github.io/test_visual_LiPMS_consistency/

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 15, 2023Jan 15, 2023

• Enolase_consistency

  Public
  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 7, 2023Jan 7, 2023

• Activation-Energy-Estimation-Workflow

  Public
  A workflow to estimate activation free energy for a protein structure obtained from a coarse-grained simulation

  simulation

  simulation

  Python

  •

  MIT License

  •00 forks•55 stars•00 issues•00 pull requests•Updated Mar 15, 2022Mar 15, 2022

• Amino-acid-pairs-position-switching-change-translation-speed

  Public
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 15, 2021Nov 15, 2021

• A-P-and-E-site-analysis

  Public
  Translation elongation rate analysis at amino acid, tRNA, and Codon level by ribosome profiling data

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 17, 2021Oct 17, 2021

• A_and_P_site_matrix_analysis_with_7_dataset_at_75-_coverage

  Public
  Translation elongation rate analysis at amino acid, tRNA, and Codon level by ribosome profiling dataset

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 2, 2021Sep 2, 2021

• P_and_A-site_pair_analysis_Complete_pipeline

  Public
  Jupyter Notebook

  •11 fork•00 stars•00 issues•00 pull requests•Updated May 7, 2021May 7, 2021

• P-site-A-site-pairs-analysis

  Public
  Data analysis workflow for the study on P-site A-site pairs

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 1, 2020Sep 1, 2020