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

pyhsmm - library for approximate unsupervised inference in Bayesian Hidden Markov Models (HMMs) and explicit-duration Hidden semi-Markov Models (HSMMs), focusing on the Bayesian Nonparametric extensions, the HDP-HMM and HDP-HSMM, mostly with weak-limit approximations.

A Survey on Deep Learning Technique for Video Segmentation

Implementation of Neonatal Seizure Detection using EEG signals for deploying on edge devices including Raspberry Pi.

A PyTorch implementation of the continual learning experiments with deep neural networks

This is official implementaion of paper "Token Shift Transformer for Video Classification".

People movement type classifier with YOLOv4 detection and SORT tracking.

YOLOv3 in PyTorch > ONNX > CoreML > TFLite

DI-smartcross - Decision Intelligence Platform for Traffic Crossing Signal Control

Accelerate Neural Net Training by Progressively Freezing Layers

Evaluation framework for testing segmentation networks in PyTorch

Face Recognize System on camera AI OAK1

Learning Logic Rules for Document-Level Relation Extraction

Implementation of CSRL from the AAAI2022 paper: Constraint Sampling Reinforcement Learning: Incorporating Expertise For Faster Learning

HiFi++: a Unified Framework for Neural Vocoding, Bandwidth Extension and Speech Enhancement

This repository contains python code necessary to replicated the experiments performed in our paper "Invariant Ancestry Search"

CLOOB: Modern Hopfield Networks with InfoLOOB Outperform CLIP

AOT (Associating Objects with Transformers) in PyTorch

A static analysis library for computing graph representations of Python programs suitable for use with graph neural networks.

PyTorch implementation of the Flow Gaussian Mixture Model (FlowGMM) model from our paper

Transfer style api - An API to use with Tranfer Style App, where you can use two image and transfer the style