ajasja

rosetta_pymol_utils

Helpful visualization in pymol for PDBs written by Rosetta

RosettaCrashCourse

Materials for Rosetta Crash Course (2022)

NGB2H

Code accompanying the article "A Multiplexed Bacterial Two-Hybrid for Rapid Characterization of Protein-Protein Interactions and Iterative Protein Design"

ddg

A DDG benchmark capture containing the benchmark dataset and benchmarked protocol captures.

domesticator_3

homooligomer_RMSD

Script to calculate RMSD between symmetric homo-oligmoers

LUMICKS_image_alignment

Scripts to align various channels based on reference beads.

af2slurm

Scripts to run AF2 with slurm integration

CC_protein_origami

Design platform for creating single-chain polyhedral cages made from coiled-coil building modules

INSRTR

Regulation of proteins using coiled-coils

af2slurm-old

Submit AlphaFold colab batch jobs to slurm

ajasja.github.io

Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes

altair

Declarative statistical visualization library for Python

DeNovoHeterodimers

Scripts and data deposition for de novo heterodimers manuscript

domesticator

files

Hosting for various files needed in notebooks and online examples

isambard

Intelligent System for Analysis, Model Building And Rational Design.

isambard-1

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

jda

Jupyter desktop application (runs a jupyter notebook server and a chromium instance).

MP3-DUET-AUTOTUNE

Data and analysis code for MP3-Seq

openmm

OpenMM is a toolkit for molecular simulation using high performance GPU code.

OrthoCCTools

Computational coiled-coil peptide design toolkit, written in modern C++

picasso

A collection of tools for painting super-resolution images

ProteinMPNN

Code for the ProteinMPNN paper

PyRosetta.notebooks

Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design

rosetta

The Rosetta Bio-macromolecule modeling package.

silent_tools

A bunch of shell utilities for dealing the silent files

Spelunking

Read definitions of in-memory Mathematica functions with ease

test_rep_1

Test repo

test_rep_2

Test_rep