Top 8 Python protein-structure Projects

Biopython

31 4,158 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 2,362 9.5 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.
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

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)
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
pypdb

1 292 5.4 Python

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

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.
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.

NOTE: The open source projects on this list are ordered by number of github stars. The number of mentions indicates repo mentiontions in the last 12 Months or since we started tracking (Dec 2020).