Python Protein-structure Resources

Introduction orfipy is a tool written in python/cython to extract ORFs in an extremely and fast and flexible manner. Other popular ORF searching tools

Introduce QML-like declarative structure to Python world. Developer writes only pure Python code for QML.

Explore RNA-Protein interactions. RNPFind is a bioinformatics tool. It takes an RNA transcript as input and gives a list of RNA binding protein (RBP)

CFN-SR A CROSS-MODAL FUSION NETWORK BASED ON SELF-ATTENTION AND RESIDUAL STRUCTURE FOR MULTIMODAL EMOTION RECOGNITION The audio-video based multimodal

ConstDict python代替的Dict数据结构 若字典不会增加字段，只读/原字段修改 使用ConstDict可节省内存 Dict()内存主要消耗的地方： 1、Dict扩容机制，预留内存空间 2、Dict也是一个对象，内部会动态维护__dict__，增加slot类属性可以节省内容 节省内存大小

Structure Information is the Key: Self-Attention RoI Feature Extractor in 3D Object Detection abstract:Unlike 2D object detection where all RoI featur

Python Example Project Structure Example of statuses that can be in readme: Visit my docs for the full documentation, examples and guides. With this p

DataStructure Journey This repo represents all we learned and are learning in Data Structure course which is based on CLRS book and is being taught by

What is liGAN? liGAN is a research codebase for training and evaluating deep generative models for de novo drug design based on 3D atomic density grid

Predicting lncRNA–protein interactions based on graph autoencoders and collaborative training Code for our paper "Predicting lncRNA–protein interactio

Hierarchical probabilistic 3D U-Net, with attention mechanisms (—𝘈𝘵𝘵𝘦𝘯𝘵𝘪𝘰𝘯 𝘜-𝘕𝘦𝘵, 𝘚𝘌𝘙𝘦𝘴𝘕𝘦𝘵) and a nested decoder structure with deep supervision (—𝘜𝘕𝘦𝘵++). Built in TensorFlow 2.5. Configured for voxel-level clinically significant prostate cancer detection in multi-channel 3D bpMRI scans.

Exploiting the Intrinsic Neighborhood Structure for Source-free Domain Adaptation (NeurIPS 2021) Code for our NeurIPS 2021 paper 'Exploiting the Intri

vs-parsedvd DVDs were an error. A wrapper for DVD file structure and ISO files. You can find me in the IEW Discord server

Unit Testing Interactions with Amazon Web Services (AWS) Unit testing AWS interactions with pytest and moto. These examples demonstrate how to structu

Offline Reverse Image Search Overview This app finds duplicate to near duplicate images by generating a hash value for each image stored with a specia

feature-set-comp Compares various time-series feature sets on computational performance, within-set structure, and between-set relationships. Reposito

peptides.py Physicochemical properties and indices for amino-acid sequences. 🗺️ Overview peptides.py is a pure-Python package to compute common descr

PyTorch implementation of the paper Ultra Fast Structure-aware Deep Lane Detection

Pixel-Perfect Structure-from-Motion (ICCV 2021 Oral) We introduce a framework that improves the accuracy of Structure-from-Motion by refining keypoint

SPDNet Structure-Preserving Deraining with Residue Channel Prior Guidance (ICCV2021) Requirements Linux Platform NVIDIA GPU + CUDA CuDNN PyTorch == 0.

Cookiecutter Data Science A logical, reasonably standardized, but flexible project structure for doing and sharing data science work. Project homepage

tetrados tetrados is a tool to generate a density of states using the linear tetrahedron method from a band structure. Currently, only VASP calculatio

SGNet Project for the IJCAI 2021 paper "Structure Guided Lane Detection" Abstract Recently, lane detection has made great progress with the rapid deve

Python example making use of best practice file structure and multithreading.

[ICCV'2021] Image Inpainting via Conditional Texture and Structure Dual Generation

A graph neural network (GNN) model to predict protein-protein interactions (PPI) with no sample features

A geometric deep learning pipeline for predicting protein interface contacts.

A simple tool that updates your pubspec.yaml file, of a Flutter project, without altering the structure of your file.

Video Autoencoder: self-supervised disentanglement of 3D structure and motion This repository contains the code (in PyTorch) for the model introduced

Table of Contents: Introduction to Torch's Tensor Library Computation Graphs and Automatic Differentiation Deep Learning Building Blocks: Affine maps,

FIDNet_SemanticKITTI Motivation Implementing complicated network modules with only one or two points improvement on hardware is tedious. So here we pr

RGN2-Replica (WIP) To eventually become an unofficial working Pytorch implementation of RGN2, an state of the art model for MSA-less Protein Folding f

Compositionally Generalizable 3D Structure Prediction In this work, We bring in the concept of compositional generalizability and factorizes the 3D sh

Recommended AWS CDK project structure for Python applications The project implements a user management backend component that uses Amazon API Gateway,

directory-structure Print a directory tree structure in your Python code. Download You can simply: pip install directory-structure Or you can also: Cl

CodeForces This repository is dedicated to my Python solutions for CodeForces problems. Feel free to copy, contribute and/or comment. If you find any

WTW-Dataset This is an official implementation for the WTW Dataset in "Parsing Table Structures in the Wild " on ICCV 2021. Here, you can download the

(ACMMM 2021 Oral) SfM Face Reconstruction Based on Massive Landmark Bundle Adjustment This repository shows two tasks: Face landmark detection and Fac

Using a predicted aligned error matrix corresponding to an AlphaFold2 model , returns a series of lists of residue indices, where each list corresponds to a set of residues clustering together into a pseudo-rigid domain.

(ACMMM 2021 Oral) SfM Face Reconstruction Based on Massive Landmark Bundle Adjustment This repository shows two tasks: Face landmark detection and Fac

Text2Event An implementation for Text2Event: Controllable Sequence-to-Structure Generation for End-to-end Event Extraction Please contact Yaojie Lu (@

ASAP-Net This project implements ASAP-Net of paper ASAP-Net: Attention and Structure Aware Point Cloud Sequence Segmentation (BMVC2020). Overview We i

Geometric Vector Perceptron Code to accompany Learning from Protein Structure with Geometric Vector Perceptrons by B Jing, S Eismann, P Suriana, RJL T

PlaneTR: Structure-Guided Transformers for 3D Plane Recovery This is the official implementation of our ICCV 2021 paper News There maybe some bugs in

Deep Two-View Structure-from-Motion Revisited This repository provides the code for our CVPR 2021 paper Deep Two-View Structure-from-Motion Revisited.

Triangle Multiplicative Module - Pytorch Implementation of the Triangle Multiplicative module, used in Alphafold2 as an efficient way to mix rows or c

PDFSyntax A Python tool to generate a static HTML file that represents the internal structure of a PDF file At some point the low-level functions deve

Invariant Point Attention - Pytorch Implementation of Invariant Point Attention as a standalone module, which was used in the structure module of Alph

ManhattanSLAM Authors: Raza Yunus, Yanyan Li and Federico Tombari ManhattanSLAM is a real-time SLAM library for RGB-D cameras that computes the camera

Plug-and-play Module Plug and play transformer you can find network structure and official complete code by clicking List The following is to quickly

Self-supervised Graph-level Representation Learning with Local and Global Structure Introduction This project is an implementation of ``Self-supervise

README clDice - a Novel Topology-Preserving Loss Function for Tubular Structure Segmentation CVPR 2021 Authors: Suprosanna Shit and Johannes C. Paetzo

ProGen - (wip) Implementation and replication of ProGen, Language Modeling for Protein Generation, in Pytorch and Jax (the weights will be made easily

SSAN Introduction This is the pytorch implementation of the SSAN model (see our AAAI2021 paper: Entity Structure Within and Throughout: Modeling Menti

kaggle-hpa-2021-7th-place-solution Code for 7th place solution of Human Protein Atlas - Single Cell Classification on Kaggle. A description of the met

SolvationAnalysis The macroscopic behavior of a liquid is determined by its microscopic structure. For ionic systems, like batteries and many enzymes,

Denoising Diffusion Probabilistic Model for Proteins Implementation of Denoising Diffusion Probabilistic Model in Pytorch. It is a new approach to gen

[TensorFlow] Protein Interface Prediction using Graph Convolutional Networks Unofficial TensorFlow implementation of Protein Interface Prediction usin

Sentance Parser Executing the Program Make sure Python 3.6+ is installed. Install requirements $ pip install requirements.txt Run the program:

ProteinLM We pretrain protein language model based on Megatron-LM framework, and then evaluate the pretrained model results on TAPE (Tasks Assessing P

ProteinBERT - Pytorch (wip) Implementation of ProteinBERT in Pytorch. Original Repository Install $ pip install protein-bert-pytorch Usage import torc

This is the repository for The Python Workshop, published by Packt. It contains all the supporting project files necessary to work through the course from start to finish.

ProteinBERT - Pytorch (wip) Implementation of ProteinBERT in Pytorch. Original Repository Install $ pip install protein-bert-pytorch Usage import torc

ProteinBERT is a universal protein language model pretrained on ~106M proteins from the UniRef90 dataset. Through its Python API, the pretrained model can be fine-tuned on any protein-related task in a matter of minutes. Based on our experiments with a wide range of benchmarks, ProteinBERT usually achieves state-of-the-art performance. ProteinBERT is built on TenforFlow/Keras.

DeepFRI Deep functional residue identification Citing @article {Gligorijevic2019, author = {Gligorijevic, Vladimir and Renfrew, P. Douglas and Koscio

The code for our newly accepted paper in Pattern Recognition 2020: "U^2-Net: Going Deeper with Nested U-Structure for Salient Object Detection."

DRO: Deep Recurrent Optimizer for Structure-from-Motion This is the official PyTorch implementation code for DRO-sfm. For technical details, please re

Graph-Based Protein Design This repo contains code for Generative Models for Graph-Based Protein Design by John Ingraham, Vikas Garg, Regina Barzilay

[Unofficial code-base] NeRF--: Neural Radiance Fields Without Known Camera Parameters [ Project | Paper | Official code base ] ⬅️ Thanks the original

Beyond Homophily in Graph Neural Networks: Current Limitations and Effective Designs Jiong Zhu, Yujun Yan, Lingxiao Zhao, Mark Heimann, Leman Akoglu,

Structural basis for solubility in protein expression systems Large-scale protein production for biotechnology and biopharmaceutical applications rely

Structure-Aware-BART This repo contains codes for the following paper: Jiaao Chen, Diyi Yang:Structure-Aware Abstractive Conversation Summarization vi

STAR-FC This code is the implementation for the CVPR 2021 paper "Structure-Aware Face Clustering on a Large-Scale Graph with 10^7 Nodes" 🌟 🌟 . 🎓 Re

NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.

Code Transformer This is an official PyTorch implementation of the CodeTransformer model proposed in: D. Zügner, T. Kirschstein, M. Catasta, J. Leskov

Prototypical Pseudo Label Denoising and Target Structure Learning for Domain Adaptive Semantic Segmentation (CVPR 2021, official Pytorch implementatio

pgmpy pgmpy is a python library for working with Probabilistic Graphical Models. Documentation and list of algorithms supported is at our official sit

Diverse Structure Inpainting ArXiv | Papar | Supplementary Material | BibTex This repository is for the CVPR 2021 paper, "Generating Diverse Structure

datatable This is a Python package for manipulating 2-dimensional tabular data structures (aka data frames). It is close in spirit to pandas or SFrame

Little Ball of Fur is a graph sampling extension library for Python. Please look at the Documentation, relevant Paper, Promo video and External Resour

NN Template Generic template to bootstrap your PyTorch project. Click on Use this Template and avoid writing boilerplate code for: PyTorch Lightning,

Meshroom is a free, open-source 3D Reconstruction Software based on the AliceVision Photogrammetric Computer Vision framework. Learn more details abou

Differentiable molecular simulation of proteins with a coarse-grained potential This repository contains the learned potential, simulation scripts and

Abstracting FastAPI Services See this article for more information: https://camillovisini.com/article/abstracting-fastapi-services/ Poetry poetry inst

trRosetta - Pytorch (wip) Implementation of trRosetta and trDesign for Pytorch, made into a convenient package

Data Structure and Algorithms with Python This repository is related to the Arabic tutorial here, within the tutorial we discuss the common data struc

Geometric Vector Perceptron Implementation of Geometric Vector Perceptron, a simple circuit with 3d rotation equivariance for learning over large biom

pgmpy pgmpy is a python library for working with Probabilistic Graphical Models. Documentation and list of algorithms supported is at our official sit

Little Ball of Fur is a graph sampling extension library for Python. Please look at the Documentation, relevant Paper, Promo video and External Resour

Python Data Structures and Algorithms This repository contains questions requiring implementation of data structures and algorithms concepts. It is us

Pythonic Data Structures and Algorithms Minimal and clean example implementations of data structures and algorithms in Python 3. Contributing Thanks f