Implementation of trRosetta and trDesign for Pytorch, made into a convenient package

Last update: Dec 17, 2022

Overview

trRosetta - Pytorch (wip)

Implementation of trRosetta and trDesign for Pytorch, made into a convenient package, for protein structure prediction and design. Will also contain an experimental version of trRosetta that uses attention. The concept of trDesign will also be abstracted into a wrapper in this repository, so that it can be applied to Alphafold2 once it is replicated. Please join the efforts there if you would like to see this happen!

The original repository can be found here

Install

$ pip install tr-rosetta-pytorch

Usage

As a command-line tool, to run a structure prediction

$ tr_rosetta <input-file.a3m>

Code

import torch
from tr_rosetta_pytorch import trRosettaNetwork

model = trRosettaNetwork(
    filters = 64,
    kernel = 3,
    num_layers = 61
).cuda()

x = torch.randn(1, 526, 140, 140).cuda()

theta, phi, distance, omega = model(x)

Citations

@article {Yang1496,
    author = {Yang, Jianyi and Anishchenko, Ivan and Park, Hahnbeom and Peng, Zhenling and Ovchinnikov, Sergey and Baker, David},
    title = {Improved protein structure prediction using predicted interresidue orientations},
    URL = {https://www.pnas.org/content/117/3/1496},
    eprint = {https://www.pnas.org/content/117/3/1496.full.pdf},
    journal = {Proceedings of the National Academy of Sciences}
}

@article {Anishchenko2020.07.22.211482,
    author = {Anishchenko, Ivan and Chidyausiku, Tamuka M. and Ovchinnikov, Sergey and Pellock, Samuel J. and Baker, David},
    title = {De novo protein design by deep network hallucination},
    URL = {https://www.biorxiv.org/content/early/2020/07/23/2020.07.22.211482},
    eprint = {https://www.biorxiv.org/content/early/2020/07/23/2020.07.22.211482.full.pdf},
    journal = {bioRxiv}
}

You might also like...

PyTorch evaluation code for Delving Deep into the Generalization of Vision Transformers under Distribution Shifts.

Out-of-distribution Generalization Investigation on Vision Transformers This repository contains PyTorch evaluation code for Delving Deep into the Gen

72 Dec 13, 2022

This package proposes simplified exporting pytorch models to ONNX and TensorRT, and also gives some base interface for model inference.

PyTorch Infer Utils This package proposes simplified exporting pytorch models to ONNX and TensorRT, and also gives some base interface for model infer

11 Mar 20, 2022

PyTorch deep learning projects made easy.

PyTorch Template Project PyTorch deep learning project made easy. PyTorch Template Project Requirements Features Folder Structure Usage Config file fo

3.8k Jan 1, 2023

Deep Learning with PyTorch made easy 🚀 !

Deep Learning with PyTorch made easy 🚀 ! Carefree? carefree-learn aims to provide CAREFREE usages for both users and developers. It also provides a c

381 Dec 22, 2022

tsai is an open-source deep learning package built on top of Pytorch & fastai focused on state-of-the-art techniques for time series classification, regression and forecasting.

Time series Timeseries Deep Learning Pytorch fastai - State-of-the-art Deep Learning with Time Series and Sequences in Pytorch / fastai

2.8k Jan 8, 2023

Kindle is an easy model build package for PyTorch.

Kindle is an easy model build package for PyTorch. Building a deep learning model became so simple that almost all model can be made by copy and paste from other existing model codes. So why code? when we can simply build a model with yaml markup file. Kindle builds a model with no code but yaml file which its method is inspired from YOLOv5.

77 Nov 11, 2022

Comments

Fixing a bug in sequence preprocessing

When cuda is available, and a sequence of length = 1 is loaded, it is left on the cpu and not copied to the gpu. That creates an error: RuntimeError: Expected all tensors to be on the same device, but found at least two devices, cuda:0 and cpu! (when checking arugment for argument tensors in method wrapper__cat)

opened by LiorZ 0
How to get a PDB file via a FASTA file?

Hello, I have recently needed to make structural predictions on many small proteins, I only have their sequence, I hope to get .PDB file, can this software implement? I tried it, it seems that I can only get the .npz file. If you can, please tell me , thank you !

opened by mooerccx 0

Implementation of trRosetta and trDesign for Pytorch, made into a convenient package

Related tags

Overview

trRosetta - Pytorch (wip)

Install

Usage

Code

Citations

You might also like...

PyTorch evaluation code for Delving Deep into the Generalization of Vision Transformers under Distribution Shifts.

This package proposes simplified exporting pytorch models to ONNX and TensorRT, and also gives some base interface for model inference.

PyTorch deep learning projects made easy.

Deep Learning with PyTorch made easy 🚀 !

tsai is an open-source deep learning package built on top of Pytorch & fastai focused on state-of-the-art techniques for time series classification, regression and forecasting.

Kindle is an easy model build package for PyTorch.

PyTorch package for the discrete VAE used for DALL·E.

Python package facilitating the use of Bayesian Deep Learning methods with Variational Inference for PyTorch

quantize aware training package for NCNN on pytorch

Comments

Fixing a bug in sequence preprocessing

How to get a PDB file via a FASTA file?

Releases(0.0.3)

0.0.3(Aug 27, 2021)

0.0.2(Feb 20, 2021)

0.0.1(Feb 5, 2021)

Owner

Phil Wang

Code for CoMatch: Semi-supervised Learning with Contrastive Graph Regularization

This package contains deep learning models and related scripts for RoseTTAFold

Video Swin Transformer - PyTorch

PyTorch implementation of the Crafting Better Contrastive Views for Siamese Representation Learning

Optimize Trading Strategies Using Freqtrade

Exploring the link between uncertainty estimates obtained via "exact" Bayesian inference and out-of-distribution (OOD) detection.

Learning from History: Modeling Temporal Knowledge Graphs with Sequential Copy-Generation Networks

This YoloV5 based model is fit to detect people and different types of land vehicles, and displaying their density on a fitted map, according to their coordinates and detected labels.

Image-to-image regression with uncertainty quantification in PyTorch

This repository contains the official MATLAB implementation of the TDA method for reverse image filtering

PyTorch implementations of the NeRF model described in "NeRF: Representing Scenes as Neural Radiance Fields for View Synthesis"

A disassembler for the RP2040 Programmable I/O State-machine!

A neuroanatomy-based augmented reality experience powered by computer vision. Features 3D visuals of the Atlas Brain Map slices.

Memory-efficient optimum einsum using opt_einsum planning and PyTorch kernels.

CS50x-AI - Artificial Intelligence with Python from Harvard University

A library for Deep Learning Implementations and utils

PyTorch implementation of DeepDream algorithm

Codes for NAACL 2021 Paper "Unsupervised Multi-hop Question Answering by Question Generation"

CVPR 2021 Official Pytorch Code for UC2: Universal Cross-lingual Cross-modal Vision-and-Language Pre-training

Unsupervised clustering of high content screen samples