Python De-novo-protein-design Resources

Molecular Docking integrated in Jupyter Notebooks Description | Citation | Installation | Examples | Limitations | License Table of content Descriptio

MkPosters Create posters using Markdown. Supports icons, admonitions, and LaTeX mathematics. At the moment it is restricted to the specific layout of

RITA: a Study on Scaling Up Generative Protein Sequence Models RITA is a family of autoregressive protein models, developed by a collaboration of Ligh

Object Detection Object detection is a computer vision task for locating instances of predefined objects in images or videos. In this tutorial, you wi

Protein GLM (wip) Implementation of a protein autoregressive language model, but with autoregressive infilling objective (editing subsequences capabil

GVP Transformer (wip) Implementation of the GVP-Transformer, which was used in the paper Learning inverse folding from millions of predicted structure

Generating 3D Molecules for Target Protein Binding This is the official implementation of the GraphBP method proposed in the following paper. Meng Liu

Molecular Nodes 🧬 🔬 💻 Buy Me a Coffee to Keep Development Going! Join a Community of Blender SciVis People! What is Molecular Nodes? Molecular Node

Description: ProtFeat is designed to extract the protein features by employing POSSUM and iFeature python-based tools. ProtFeat includes a total of 39

RL - EmsPy (work In Progress...) The EmsPy Python package was made to facilitate Reinforcement Learning (RL) algorithm research for developing and tes

Ontoseer This document provides documentation for the first version of OntoSeer.OntoSeer is a tool that monitors the ontology development process andp

EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein

B4PPI Benchmarking Pipeline for the Prediction of Protein-Protein Interactions How this benchmarking pipeline has been built, and how to use it, is de

GeneDisco is a benchmark suite for evaluating active learning algorithms for experimental design in drug discovery.

GeneDisco ICLR-22 Challenge Starter Repository The starter repository for submissions to the GeneDisco challenge for optimized experimental design in

polyprotein_stats A small tool to test and visualize protein embeddings and amino acid proportions. Currently deployed on streamlit.io. Given a set of

RegNet Pytorch Implementation of "Desigining Network Design Spaces", Radosavovic et al. CVPR 2020. Paper | Official Implementation RegNet offer a very

Source code for EquiDock: Independent SE(3)-Equivariant Models for End-to-End Rigid Protein Docking (ICLR 2022) Please cite "Independent SE(3)-Equivar

Multiplayer game (enter the number closest to the average) Design Client-Server design The client's side is responsible for sending numbers from the g

Building a Mario-like, classic platformer game in Python using the PyGame Library

Awesome AI for Art & Design An awesome list of AI for art and design - resources, and popular datasets and how we may apply computer vision tasks to a

Reso Reso is a low-level circuit design language and simulator, inspired by things like Redstone, Conway's Game of Life, and Wireworld. What is Reso?

Iterative refinement graph neural network for antibody sequence-structure co-des

Project1_Next-Quarter-Game-Design-Prediction What games should I design next quarter? 상황 : 게임회사 데이터팀 합류 문제 : '다음 분기에 어떤 게임을 설계해야할까' Data Description N

GNN_PPI Codes and models for the paper "Learning Unknown from Correlations: Graph Neural Network for Inter-novel-protein Interaction Prediction". Lear

MLOps The MLOps is the process of continuous integration and continuous delivery of Machine Learning artifacts as a software product, keeping it insid

Evolution Gym A large-scale benchmark for co-optimizing the design and control of soft robots. As seen in Evolution Gym: A Large-Scale Benchmark for E

OntoProtein This is the implement of the paper "OntoProtein: Protein Pretraining With Ontology Embedding". OntoProtein is an effective method that mak

ReLSO Improved Fitness Optimization Landscapes for Sequence Design Description Citation How to run Training models Original data source Description In

Differences in this GUI program : Default titlebar removed Custom Minimize,Maximize and Close Buttons Drag & move window from any point Program work l

Generative design of breakwaters usign deep convolutional neural network as a surrogate model This repository contains the code for the paper "Generat

PROTEIN-EXPRESSION-ANALYSIS-FOR-DOWN-SYNDROME Down syndrome (DS) is a chromosomal disorder where organisms have an extra chromosome 21, sometimes know

Overview This repository hosts the official PyTorch implementation of the paper: "HairCLIP: Design Your Hair by Text and Reference Image". Our single

Rbc-traps-generative-design - The generative design for single red clood cell hydrodynamic traps using GEFEST framework

Transform application Lifecycle Data and Design and ETL pipeline architecture for ingesting data from multiple sources to redshift This project is composed of two parts: Part1 and Part2

Computational Design and Dynamics of Soft Systems · This is a repository that contains the source code for generating the lecture notes, handouts, exe

Aircraft design optimization made fast through modern automatic differentiation. Plug-and-play analysis tools for aerodynamics, propulsion, structures, trajectory design, and much more.

RFDesign: Protein hallucination and inpainting with RoseTTAFold Jue Wang (juewan

A 3D Generative Model for Structure-Based Drug Design Coming soon... Citation @inproceedings{luo2021sbdd, title={A 3D Generative Model for Structu

To Design and Implement Logistic Regression to Classify Between Benign and Malignant Cancer Types, from a Database Taken From Dr. Wolberg reports his Clinic Cases.

The GUI application by Python3.8. Using QT Design draw UI and generator UI XML file provides to PySide2 build GUI components. Total adopt OOD design class, service, and abstract class. OOP implemented this project.

To design and implement the Identification of Iris Flower species using machine learning using Python and the tool Scikit-Learn.

About visualapplets.py The Basler AG company provides a TCL scripting engine to automatize the creation of VisualApplets designs (a former Silicon Sof

icontract icontract provides design-by-contract to Python3 with informative violation messages and inheritance. It also gives a base for a flourishing

Passport-Recogniton-System This is a passport scanning web service to help you scan, identify and validate your passport created with a simple and fle

Design-Bench Design-Bench is a benchmarking framework for solving automatic design problems that involve choosing an input that maximizes a black-box

This is not an official Google product ml-design-patterns Source code accompanying O'Reilly book: Title: Machine Learning Design Patterns Authors: Val

Introduction 关键点版本：已完成 全景分割版本：已完成 实例分割版本：已完成 YOLOX is an anchor-free version of

CustomTkinter With CustomTkinter you can create modern looking user interfaces in python with tkinter. CustomTkinter is a tkinter extension which prov

Are you tired of using visualization software, or full blown suites just to separate protein chains / ligands ? Are you tired of organizing the mess o

Electrical Network Analyzer A simple electrical network analyzer. Given the oriented graph of the electrical network (circut), BASED ON computer-aided

This program analyzes a DNA sequence and outputs snippets of DNA that are likely to be protein-coding genes.

Simple and Robust Loss Design for Multi-Label Learning with Missing Labels Official PyTorch Implementation of the paper Simple and Robust Loss Design

A Python library for design by contract (DbC) and checking values, exceptions, and side-effects. In a nutshell, deal empowers you to write bug-free co

Flask Paper Kit Open-Source Web App coded in Flask Framework - Provided by AppSeed Web App Generator. App Features: SQLite database SQLAlchemy ORM Ses

py-object-factory objectfactory is a python package to easily implement the factory design pattern for object creation, serialization, and polymorphis

What is jawanndenn? jawanndenn is a simple web application to schedule meetings and run polls, a libre alternative to Doodle. It is using the followin

AWS RoseTTAFold Infrastructure template and Jupyter notebooks for running RoseTTAFold on AWS Batch. Overview Proteins are large biomolecules that play

Py-MADCAD it's time to throw parametric softwares out ! Simple yet powerful CAD (Computer Aided Design) library, written with Python. Installation

Flask Boilerplate - Material Kit Design | AppSeed

Django Boilerplate - Material Kit Design | AppSeed

Pundit Pundit provides a set of helpers which guide you in leveraging regular Ruby classes and object oriented design patterns to build a simple, robu

Overview This repository hosts the official PyTorch implementation of the paper: "HairCLIP: Design Your Hair by Text and Reference Image". Our single

Uni-Fold: Training your own deep protein-folding models. This package provides and implementation of a trainable, Transformer-based deep protein foldi

Trapper (Transformers wRAPPER) Trapper is an NLP library that aims to make it easier to train transformer based models on downstream tasks. It wraps h

SECSE SECSE: Systemic Evolutionary Chemical Space Explorer Chemical space exploration is a major task of the hit-finding process during the pursuit of

This is code of RID-Noise. Reproduce RID-Noise Results Toy tasks Please refer to the notebook ridnoise.ipynb to view experiments on three toy tasks. B

Unofficial implementation of "Coordinate Attention for Efficient Mobile Network Design". CoordAttention tensorflow slim

Uni-Fold: Training your own deep protein-folding models. This package provides an implementation of a trainable, Transformer-based deep protein foldin

MIDI Language Introduction Reference Paper: Pop Music Transformer: Beat-based Modeling and Generation of Expressive Pop Piano Compositions: code This

Decoding the Protein-ligand Interactions Using Parallel Graph Neural Networks Requirements python 0.10+ rdkit 2020.03.3.0 biopython 1.78 openbabel 2.4

Explicable Reward Design for Reinforcement Learning Agents [NeurIPS'21]

FAU - Colors The official colors of Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) as matplotlib / seaborn colormaps. We support the old colo

Testability-Aware Low Power Controller Design with Evolutionary Learning This repo contains the source code of Testability-Aware Low Power Controller

Problem statements on System Design and Software Architecture as part of Arpit's System Design Masterclass

Image Tooᥣs Bot I specialize for logo design Services with Amazing logo Creator Platform and more tools

PRIP PRIP：A Protein-RNA Interface Predictor Based on Semantics of Sequences installation gensim==3.8.3 matplotlib==3.1.3 xgboost==1.3.3 prettytable==2

trRosetta This package is a part of trRosetta protein structure prediction protocol developed in: Improved protein structure prediction using predicte

Design and build a wrapper for the Open Weather API current weather data service that returns a city's temperature, with caching, also allowing for the temperature of the latest queried cities that are still validly cached to be retrieved.

Differential_Privacy_CPS Python implementation of the research paper Leveraging Unique CPS Properties to Design Better Privacy-Enhancing Algorithms Re

English | 简体中文 Latest News 2021.10.25 Paper "Docking-based Virtual Screening with Multi-Task Learning" is accepted by BIBM 2021. 2021.07.29 PaddleHeli

Cooperative multi-agent reinforcement learning for high-dimensional nonequilibrium control Official implementation of: Cooperative multi-agent reinfor

Breakout Software Design Final Project, Spring 2020 Team members: Izumi, Lilo For our Interactive Visualization, we implemented the classic arcade gam

gdsfactory 3.5.5 gdsfactory is an EDA (electronics design automation) tool to Layout Integrated Circuits. It is build on top of phidl gdspy and klayou

JLC2KiCad_lib is a python script that generate a component library (schematic, footprint and 3D model) for KiCad from the JLCPCB/easyEDA library. This script requires Python 3.6 or higher.

Polypharmacy - DDI - Synergy Survey The Survey Paper This repository accompanies our survey paper A Unified View of Relational Deep Learning for Polyp

System Design Assignments The repository contains a set of problem statements around Software Architecture and System Design as conducted by Arpit's S

Pyslvs-UI A GUI-based (PyQt5) tool used to design 2D linkage mechanism. Planar Linkages Simulation Python-Solvespace: Kernel from Solvespace with Cyth

Music Tools Set of utility tools for Spotify and Last.fm. Built on my other libraries for Spotify (spotframework), Last.fm (fmframework) and interfaci

This package is a python library with tools for the Molecular Simulation - Software Gromos. It allows you to easily set up, manage and analyze simulations in python.

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

Python Youtube Downloader GUI This is a GUI application that allows you to download videos from Youtube. Features Download videos from Youtube in MP3

Styled text-to-drawing synthesis method. Featured at the 2021 NeurIPS Workshop on Machine Learning for Creativity and Design

Autonomous Ground Vehicle Navigation and Control Simulation Examples in Python THIS PROJECT IS CURRENTLY A WORK IN PROGRESS AND THUS THIS REPOSITORY I

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)

Polypharmacy - DDI - Synergy Survey The Survey Paper This repository accompanies our survey paper A Unified View of Relational Deep Learning for Polyp

Implicit Deep Adaptive Design (iDAD) This code supports the NeurIPS paper 'Implicit Deep Adaptive Design: Policy-Based Experimental Design without Lik

Multi-Tool-v1.0 Discord Multi Tool that focuses on design and easy usage Delete webhook Block all friends Spam webhook Modify webhook Webhook info Tok

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

Machine Learning Systems Design Read this booklet here. This booklet covers four main steps of designing a machine learning system: Project setup Data