Repositories list

• AlloCraft

  Public
  Allosteric design of proteins using allosteric pathways, stability calculations, and normal mode analysis

  MATLAB

  •

  Mozilla Public License 2.0

  •1•5•0•0•Updated Dec 19, 2025Dec 19, 2025

• AlloDy

  Public
  Analysis of molecular dynamics trajectories of proteins, with a focus on allosteric pathways and ensemble differences

  MATLAB

  •

  Mozilla Public License 2.0

  •2•7•0•0•Updated Dec 10, 2025Dec 10, 2025

• AlloPool

  Public
  Python

  •0•1•1•0•Updated Sep 5, 2025Sep 5, 2025

• Dimeric_MultiDomain_Biosensor_Builder

  Public
  Assembly procotol to construct dimeric chimeras built from diverse structural native monomeric units, coupling orthgonal input/output signals.

  Roff

  •

  GNU General Public License v3.0

  •1•1•1•0•Updated Jun 27, 2025Jun 27, 2025

• SPaDES_DESIGNS

  Public
  Repo containing demo to recreate Ion Sampling and designs discussed in 2023 Rosetta SPaDES submission

  Python

  •0•4•0•0•Updated Jan 24, 2025Jan 24, 2025

• phenix_with_spades

  Public
  Demo to replicate results from submitted article on combining phenix with spades for improved structure refinement

  Python

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Jan 24, 2025Jan 24, 2025

• MDprot

  Public
  A set of Matlab functions to analyze protein structures and molecular dynamics (MD) simulations of proteins

  MATLAB

  •

  Mozilla Public License 2.0

  •3•2•0•0•Updated Jun 20, 2024Jun 20, 2024

• biophysics

  Public
  Library and tools for parsing and modifying biophysical files.

  D

  •

  Mozilla Public License 2.0

  •1•1•0•0•Updated Jan 15, 2024Jan 15, 2024

• CAPSens_design

  Public
  Python

  •0•3•0•0•Updated Mar 7, 2023Mar 7, 2023

• QUESTS

  Public
  Quaternary receptor state design for signaling selectivity

  Python

  •0•2•0•0•Updated Oct 10, 2022Oct 10, 2022