P2Rank: Protein-ligand binding site prediction from protein structure based on machine learning.

• UpdatedOct 4, 2025
• Groovy

macromolecular crystallography library and utilities

• UpdatedNov 3, 2025
• C++

A library to open/edit/save (crystallographic) Protein Data Bank (PDB) and mmCIF files in Rust.

• UpdatedAug 19, 2025
• Rust

Benchmarking common tasks on proteins in various languages and packages

• UpdatedDec 27, 2020
• Python

Library containing code to manipulate mmCIF and PDB files

• UpdatedNov 5, 2025
• C++

Python snippets for PyMOL to be run in Jupyterlab via the jupyterlab-snippets-multimenus extension.

• UpdatedMay 9, 2024
• HTML

📖 mmCIF support for hybrid/integrative models

• UpdatedJun 3, 2025
• Shell

👋 Webserver & command-line tool for search of APO (unbound) protein structures from HOLO (bound) forms and vice versa.http://apoholo.cz

• UpdatedJun 14, 2024

Protein Structure Archiver

• UpdatedSep 10, 2025
• C++

Program to plot a Ramachandran plot of all dihedral angles from a given PDB file. Background is empirically generated from the peptides in the Top8000 PDB data set.

• UpdatedFeb 25, 2025
• Jupyter Notebook

📦 A Command Line Tool for downloading protein structures, sequences and MSAs

• UpdatedNov 21, 2017
• Python

Search PDB by elements.

• UpdatedNov 2, 2022
• JavaScript

Super lightweight and fast mmCIF/PDB/MOL2 file parser into Pandas DataFrames and backwards writer.

• UpdatedOct 20, 2025
• Python

Supports the use of PyMOL in literate programming in org-mode, which is best run in Emacs.

• UpdatedMay 13, 2024
• YASnippet

Benchmarks for reading and interpreting mmCIF files

• UpdatedAug 30, 2021
• Python

Convert in batch CIF files to PDB

• UpdatedOct 27, 2023
• Python

Parser for mmCIF files in Nim

• UpdatedAug 24, 2025
• Python

A small, developer-friendly 3D molecule viewer for the modern web

• UpdatedMay 27, 2018
• JavaScript

Open-source framework for simple and fast integration of protein structure data with sequence annotations and genetic variation

• UpdatedMar 1, 2024
• Python

Parts of Gemmi in WebAssembly.

• UpdatedJan 18, 2025
• HTML