Repositories list

• protein-design-archive

  Public
  Source code for The Protein Design Archive web application.

  Elm

  •1•1•28•1•Updated Jan 5, 2025Jan 5, 2025

• chronowska-stam-wood-2024-protein-design-archive

  Public
  Code supporting the Protein Design Archive (PDA) database publication

  Jupyter Notebook

  •

  MIT License

  •0•5•0•1•Updated Jan 5, 2025Jan 5, 2025

• adaptyv-bio-analysis

  Public
  HTML

  •0•1•0•0•Updated Dec 19, 2024Dec 19, 2024

• drMD

  Public
  Molecular Dynamics for Experimentalists

  Python

  •

  MIT License

  •1•22•1•0•Updated Dec 10, 2024Dec 10, 2024

• drFrankenstein

  Public
  Fast Parameterisation of Complex Molecules for the AMBER forcefield

  Jupyter Notebook

  •0•1•0•0•Updated Dec 4, 2024Dec 4, 2024

• isambard

  Public
  Intelligent System for Analysis, Model Building And Rational Design of biomolecules.

  Python

  •

  MIT License

  •7•1•0•0•Updated Nov 20, 2024Nov 20, 2024

• wells-wood-research.github.io

  Public
  Group website.

  Elm

  •0•0•0•7•Updated Nov 12, 2024Nov 12, 2024

• ampal

  Public
  A simple, intuitive and Pythonic framework for representing biomolecular structure.

  Python

  •

  MIT License

  •4•0•0•0•Updated Oct 26, 2024Oct 26, 2024

• timed-design

  Public
  Protein Sequence Design with Deep Learning and Tooling like Monte Carlo Sampling and Analysis

  proteinprotein-design

  Python

  •11•53•8•1•Updated Oct 24, 2024Oct 24, 2024

• de-stress

  Public
  DE-STRESS is a model evaluation pipeline that aims to make protein design more reliable and accessible.

  bioinformaticspipelinestructural-biology+ 4protein-structureproteinwebappprotein-design

  C++

  •1•19•10•8•Updated Jul 25, 2024Jul 25, 2024

• aposteriori

  Public
  DNN based protein design.

  Python

  •

  MIT License

  •2•7•4•1•Updated Jul 15, 2024Jul 15, 2024

• TTSCP_L102C_DSB-MBnThz-vs-TTSCP_L102C_DDSB-MBnThz

  Public
  Python

  •0•1•0•0•Updated May 2, 2024May 2, 2024

• BAlaS

  Public
  Source code for the BUDE Alanine Scan web application.

  Elm

  •3•9•1•1•Updated Apr 8, 2024Apr 8, 2024

• stam-m-large-scale-analysis-2024

  Public
  Python

  •0•0•0•0•Updated Mar 21, 2024Mar 21, 2024

• oshea-j-wood-c-pbp-design-2023

  Public
  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Jan 18, 2024Jan 18, 2024

• ccbuilder2

  Public
  A web application for atomistic modelling of coiled coils and collagens.

  Elm

  •

  MIT License

  •3•0•0•0•Updated Nov 22, 2023Nov 22, 2023

• pdb-compare

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Nov 21, 2023Nov 21, 2023

• ProteinMPNN_custom_training

  Public
  Scripts for training ProteinMPNN with a custom dataset and other utils

  Shell

  •0•2•0•0•Updated Oct 27, 2023Oct 27, 2023

• PDBench

  Public
  PDBench is a dataset and software package for evaluating fixed-backbone sequence design algorithms.

  deep-learningproteinsprotein-structure+ 1protein-design

  Python

  •

  MIT License

  •0•27•4•0•Updated Jan 17, 2023Jan 17, 2023

• pv

  Public
  WebGL protein viewer

  JavaScript

  •

  MIT License

  •84•0•0•0•Updated Oct 11, 2021Oct 11, 2021

• pollen

  Public
  Jupyter Notebook

  •

  MIT License

  •1•0•0•0•Updated Aug 24, 2021Aug 24, 2021

• alphafold2-multiprocessing

  Public
  Use AlphaFold by Deep Mind in Batch Mode + Multiprocessing

  multiprocessingalphafold

  Python

  •1•22•2•0•Updated Aug 5, 2021Aug 5, 2021

• stam-m-wood-c-de-stress-2021

  Public
  Python

  •0•1•0•0•Updated Aug 5, 2021Aug 5, 2021

• oshea-j-interface-engineering-2021

  Public
  DIGITAL Command Language

  •

  MIT License

  •0•3•0•0•Updated Apr 16, 2021Apr 16, 2021

• galloway-jg-hairpin-self-assembly-2020

  Public
  Scripts and data for running particle analysis on AFM data

  Jupyter Notebook

  •

  MIT License

  •0•2•0•0•Updated Jul 9, 2020Jul 9, 2020

• elm-molecules

  Public
  An Elm package for working with molecular structure.

  Elm

  •

  MIT License

  •0•1•1•0•Updated Jun 29, 2020Jun 29, 2020