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alphafold

Open source code for AlphaFold.

autodock-vina

AutoDock Vina

blueprint_builder_demo

This repository contains the demonstrations prepared for report 'De novo protein design using the blueprint builder in Rosetta'.

ccbuilder2

A web application for atomistic modelling of coiled coils and collagens.

code_my

python_code used

colabfold

Making Protein folding accessible to all via Google Colab!

eternabrain

Deep learning to solve RNA design puzzles

funfoldesdata

Rosetta FunFolDes – a general framework for the computational design of functional proteins.

gpt_academic

为GPT/GLM等LLM大语言模型提供实用化交互接口，特别优化论文阅读/润色/写作体验，模块化设计，支持自定义快捷按钮&函数插件，支持Python和C++等项目剖析&自译解功能，PDF/LaTex论文翻译&总结功能，支持并行问询多种LLM模型，支持chatglm3等本地模型。接入通义千问, deepseekcoder, 讯飞星火, 文心一言, llama2, rwkv, claude2, moss等。

gpt_api_free

Free ChatGPT API Key，免费ChatGPT API，支持GPT4 API（免费），ChatGPT国内可用免费转发API，直连无需代理。可以搭配ChatBox等软件/插件使用，极大降低接口使用成本。国内即可无限制畅快聊天。

isambard-1

Intelligent System for Analysis, Model Building And Rational Design of biomolecules.

jerkwin.github.io

lineardesign

The LinearDesign mRNA design software.

localcolabfold

ColabFold on your local PC

minigpt-4

MiniGPT-4: Enhancing Vision-language Understanding with Advanced Large Language Models

papers_for_protein_design_using_dl

List of papers about Proteins Design using Deep Learning

plip

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Adasme et al. (2021), https://doi.org/10.1093/nar/gkab294

pointsite

PointSite: a point cloud segmentation tool for identification of protein ligand binding atoms

protcad

protein-design-tutorials

Tutorials, cheat sheets, and other resources for computational methods for protein design.

proteinmpnn

Code for the ProteinMPNN paper

pyrosetta-basic

pyrosetta.notebooks

Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design

rfdiffusion

Code for running RFdiffusion

ribosome-binding-site-calculator-v1.0

The Ribosome Binding Site (RBS) Calculator can predict the translation initiation rate of a protein coding sequence in bacteria and design synthetic RBS sequences to rationally control the translation initiation rate. It is used to design synthetic biological systems.

rosettafold

This package contains deep learning models and related scripts for RoseTTAFold

scaffold_design