RFDesign - Protein hallucination and inpainting with RoseTTAFold

Related tags

MiscellaneousRFDesign
Overview

RFDesign: Protein hallucination and inpainting with RoseTTAFold

Jue Wang ([email protected])
Doug Tischer ([email protected])
Sidney Lisanza ([email protected])
David Juergens ([email protected])
Joe Watson ([email protected])

This repository contains code for protein hallucination or inpainting, as described in our preprint. Code for postprocessing and analysis scripts included in scripts/.

License

All code is released under the MIT license.

All weights for neural networks are released for non-commercial use only under the Rosetta-DL license.

Installation

  1. Clone the repository:
    git clone https://git.ipd.uw.edu/jue/rfdesign.git
    cd rfdesign
  1. Create environment and install dependencies:
    cd envs
    conda env create -f SE3.yml
  1. Download model weights (see license info above).
    wget https://files.ipd.uw.edu/pub/rfdesign/weights.tar.gz
    tar xzf weights.tar.gz
  1. Configure path to weights. Put a file called config.json in hallucination/ and inpainting/ with the path to the weights directory. An example file is in each folder to copy from.

Dependencies

If you want/need to configure your environment manually, here are the packages in our environment:

Notes

  • If you are running this on digs at the IPD, you don't need to do steps 3-4.
  • If you are getting output pdbs that are a ball of disconnected segments (as viewed in pymol), this may be due to a problem with the spherical harmonics cached by SE3-transformer. A workaround is to copy the hallucination/cache/ folder (a correct, clean copy of the cache) to your working directory before running hallucinate.py or inpaint.py.

Usage

See READMEs in hallucination/ and inpainting/ subfolders.

References

J. Wang, S. Lisanza, D. Juergens, D. Tischer, et al. Deep learning methods for designing proteins scaffolding functional sites. bioRxiv (2021). link

M. Baek, et al., Accurate prediction of protein structures and interactions using a three-track neural network, Science (2021). link

An earlier version of our hallucination method can be found at the trdesign-motif repo and published at:

D. Tischer, S. Lisanza, J. Wang, R. Dong, I. Anishchenko, L. F. Milles, S. Ovchinnikov, D. Baker. Design of proteins presenting discontinuous functional sites using deep learning. (2020) bioRxiv link

Our work is based on previous hallucination methods for unconstrained protein generation and fixed-backbone sequence design (trDesign repo):

I Anishchenko, SJ Pellock, TM Chidyausiku, ..., S Ovchinnikov, D Baker. De novo protein design by deep network hallucination. (2021) Nature link

C Norn, B Wicky, D Juergens, S Liu, D Kim, B Koepnick, I Anishchenko, Foldit Players, D Baker, S Ovchinnikov. Protein sequence design by conformational landscape optimization. (2021) PNAS link

LinkML based SPARQL template library and execution engine

sparqlfun LinkML based SPARQL template library and execution engine modularized core library of SPARQL templates generic templates using common vocabs

Linked data Modeling Language 6 Oct 10, 2022
Step by step development of a vending coffee machine project, including tkinter, sqlite3, simulation, etc.

Step by step development of a vending coffee machine project, including tkinter, sqlite3, simulation, etc.

Nikolaos Avouris 2 Dec 05, 2021
WordlistPasswordGenerator - Shuhfab Basheer

WordlistPasswordGenerator - Shuhfab Basheer Python wordlist generator MAINTAINER

1 Dec 31, 2021
Short, introductory guide for the Python programming language

100 Page Python Intro This book is a short, introductory guide for the Python programming language.

Sundeep Agarwal 185 Dec 26, 2022
Multiperiod Reports by Month/Quarter/Year in Beancount.

Multiperiod Reports by Month/Quarter/Year in Beancount. Plotting income and expenses over time. Treemap plot of expenses.

Altynbek Isabekov 16 Aug 13, 2022
Telegram bot to remove the forwarded tag from messages.

Anonymous Sender Bot @AnonySendBot Telegram bot to remove the forwarded tag from messages. Table of Contents Usage Deploy To Heroku Local Deploying En

Stark Bots 26 Nov 24, 2022
AIO solution for SSIS students

ssis.bit AIO solution for SSIS students Hardware CircuitPython supports more than 200 different boards. Locally available is the TTGO T8 ESP32-S2 ST77

3 Jun 05, 2022
A general illumination correction method for optical microscopy.

CIDRE About CIDRE is a retrospective illumination correction method for optical microscopy. It is designed to correct collections of images by buildin

Kevin Smith 31 Sep 07, 2022
Small tool to use hero .json files created with Optolith for The Dark Eye/ Das Schwarze Auge 5 to perform talent probes.

DSA5-ProbeMaker A little tool for The Dark Eye 5th Edition (Das Schwarze Auge 5) to load .json from Optolith character generation and easily perform t

2 Jan 06, 2022
Very Simple Zoom Spam Pinger!

Very Simple Zoom Spam Pinger!

Syntax. 2 Mar 05, 2022
A set of decks and notebooks with exercises for use in a hands-on causal inference tutorial session

intro-to-causal-inference A introduction to causal inference using common tools from the python data stack Table of Contents Getting Started Install g

Roni Kobrosly 15 Dec 07, 2022
An open letter in support of Richard Matthew Stallman being reinstated by the Free Software Foundation

An open letter in support of RMS. To sign, click here and name the file username.yaml (replace username with your name) with the following content

2.4k Jan 07, 2023
This program can calculate the Aerial Distance between two cities.

Aerial_Distance_Calculator This program can calculate the Aerial Distance between two cities. This repository include both Jupyter notebook and Python

InvisiblePro 1 Apr 08, 2022
Fixed waypoint(pose) navigation for turtlebot simulation.

Turtlebot-NavigationStack-Fixed-Waypoints fixed waypoint(pose) navigation for turtlebot simulation. Task Details Task Permformed using Navigation Stac

Shanmukha Vishnu 1 Apr 08, 2022
Web3 Solidity Connector

With this project, you can compile your sol files and create new transactions including creating contract and calling the state changer functions. You can integrate integrate your sol files with Pyth

Fethi Tekyaygil 3 Oct 09, 2022
Ontario-Covid19-Screening - An automated Covid-19 School Screening Tool for Ontario

Ontario-Covid19-Screening An automated Covid-19 School Screening Tool for Ontari

Rayan K 0 Feb 20, 2022
Plugins for Agisoft Metashape

Данные плагины предназначены для расширения функциональных возможностей Agisoft Metashape. Плагины представляют собой отдельные программы с собственным интерфейсом, которые запускаются внутри Agisoft

GeoScan 17 Dec 10, 2022
An OpenSource crowd-sourced cooking recipes website

An OpenSource crowd-sourced cooking recipes website

21 Jul 31, 2022
An example file showing a simple endpoints like a login/logout function and maybe some others.

Flask API Example An example project showing a simple endpoints like a login/logout function and maybe some others. How to use: Open up your IDE (or u

Kevin 1 Oct 27, 2021
Open source home automation that puts local control and privacy first

Home Assistant Open source home automation that puts local control and privacy first. Powered by a worldwide community of tinkerers and DIY enthusiast

Home Assistant 57k Jan 02, 2023