Top 18 protein-structure Open-Source Projects

• Biopython

  31 4,167 9.6 Python

  Official git repository for Biopython (originally converted from CVS)

  

Project mention: Invitación a proyecto - Biopython en Español | /r/devsarg | 2023-07-23

• openfold

  3 2,378 9.4 Python

  Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

  

Project mention: TIL : about the game "Foldit", a puzzle game about protein folding. In 2011, its gamers helped decipher a protein of a HIV-like virus, solving a scientific problem that went unsolved for 15 years in as little as 10 days. | /r/todayilearned | 2023-05-22

Seeing this stuff on GitHub is mind-blowing: https://github.com/aqlaboratory/openfold

• InfluxDB

  www.influxdata.com sponsored

  Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.

  

• graphein

  2 978 7.8 Jupyter Notebook

  Protein Graph Library

• MolecularNodes

  2 785 9.8 Python

  Toolbox for molecular animations in Blender, powered by Geometry Nodes.

Project mention: Rendering protein structures inside cells at the atomic level with Unreal Engine | news.ycombinator.com | 2024-02-29

• foldseek

  1 632 9.3 C

  Foldseek enables fast and sensitive comparisons of large structure sets.

  

• tape

  1 620 0.0 Python

  Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology. (by songlab-cal)

  

• BioJava

  2 575 8.2 Java

  :book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.

  

Project mention: Outperforming Rust DNA sequence parsing benchmarks by 50% with Mojo | news.ycombinator.com | 2024-02-08

Here is a cache of valid and invalid FASTQ files for unit tests

https://github.com/biojava/biojava/tree/master/biojava-genom...

• WorkOS

  workos.com sponsored

  The modern identity platform for B2B SaaS. The APIs are flexible and easy-to-use, supporting authentication, user identity, and complex enterprise features like SSO and SCIM provisioning.

  

• hh-suite

  2 498 0.0 C

  Remote protein homology detection suite.

  

• EquiBind

  2 452 0.0 Python

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

• bio_embeddings

  1 434 0.0 HTML

  Get protein embeddings from protein sequences

• Molly.jl

  1 365 9.4 Julia

  Molecular simulation in Julia

  

• pypdb

  1 292 5.4 Python

  A Python API for the RCSB Protein Data Bank (PDB)

• awesome-AI-based-protein-design

  1 182 3.7

  A collection of research papers for AI-based protein design

  

• deepblast

  2 96 4.8 Python

  Neural Networks for Protein Sequence Alignment

  

Project mention: [D] To all the machine learning engineers: most difficult model task/type you’ve ever had to work with? | /r/MachineLearning | 2023-07-03

• hPDB

  0 20 0.0 Haskell

  PDB parser in Haskell

  

• awesome-protein-design

  1 10 0.0

  A curated list of awesome protein design research, software and resources.

• ProteinStructurePrediction

  1 9 0.0 Python

  Protein structure prediction is the task of predicting the 3-dimensional structure (shape) of a protein given its amino acid sequence and any available supporting information. In this section, we will Install and inspect sidechainnet, a dataset with tools for predicting and inspecting protein structures, complete two simplified implementations of Attention based Networks for predicting protein angles from amino acid sequences, and visualize our predictions along the way.

• MetaBioCargo

  1 0 0.0 Rust

  Meta-Bio-Cargo predict #Ru-Bi-CO-S protein

  

• SaaSHub

  www.saashub.com sponsored

  SaaSHub - Software Alternatives and Reviews. SaaSHub helps you find the best software and product alternatives

  

protein-structure related posts

• Rendering protein structures inside cells at the atomic level with Unreal Engine
  2 projects | news.ycombinator.com | 29 Feb 2024
• Outperforming Rust DNA sequence parsing benchmarks by 50% with Mojo
  1 project | news.ycombinator.com | 8 Feb 2024
• TIL : about the game "Foldit", a puzzle game about protein folding. In 2011, its gamers helped decipher a protein of a HIV-like virus, solving a scientific problem that went unsolved for 15 years in as little as 10 days.
  5 projects | /r/todayilearned | 22 May 2023
• [P] Detailed Explanation of how AlphaFold Works, Protein Folding and Design
  1 project | /r/MachineLearning | 11 Mar 2023
• Meet Graphein: a Python Library for Geometric Deep Learning and Network Analysis on Protein Structures and Interaction Networks
  1 project | /r/machinelearningnews | 27 Jan 2023
• GeneWarrior (DNA sequence manipulation web app) is now open source
  2 projects | /r/java | 7 Jan 2023
• [R] EquiBind: Geometric Deep Learning for Drug Binding Structure Prediction
  1 project | /r/MachineLearning | 16 Jul 2022
• A note from our sponsor - SaaSHub
  www.saashub.com | 26 Apr 2024

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