A Python API for the RCSB Protein Data Bank (PDB)
☆335Jun 12, 2026Updated this week
Alternatives and similar repositories for pypdb
Users that are interested in pypdb are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- A dependency-free cross-platform swiss army knife for PDB files.☆455Jun 10, 2026Updated last week
- Interaction Fingerprints for protein-ligand complexes and more☆504Updated this week
- A Python Package for Protein Dynamics Analysis☆549Jun 8, 2026Updated last week
- PDBFixer fixes problems in PDB files☆657Mar 10, 2026Updated 3 months ago
- C-library for calculating Solvent Accessible Surface Areas☆194May 31, 2026Updated 2 weeks ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Working with molecular structures in pandas DataFrames☆752May 22, 2026Updated 3 weeks ago
- MoleculeKit: Your favorite molecule manipulation kit☆237Updated this week
- Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Schake,…☆689Oct 30, 2025Updated 7 months ago
- PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.☆361Mar 21, 2026Updated 2 months ago
- The OpenMM Cookbook and Tutorials☆57Apr 28, 2026Updated last month
- Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design☆698Feb 27, 2026Updated 3 months ago
- Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm☆399Sep 16, 2025Updated 9 months ago
- A Python library for structural cheminformatics☆109Nov 18, 2025Updated 7 months ago
- An all-atom protein structure dataset for machine learning.☆364Mar 16, 2024Updated 2 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- HTMD: Programming Environment for Molecular Discovery☆274Jun 8, 2026Updated last week
- Protein-Ligand Benchmark Dataset for Free Energy Calculations☆224Jul 29, 2024Updated last year
- Python macromolecular parsing (with .pdb/.cif/.mmtf parsing and production)☆106Dec 7, 2023Updated 2 years ago
- A set of tools for manipulating and doing calculations on wwPDB macromolecule structure files☆179Oct 10, 2019Updated 6 years ago
- // PROJECT PAUSED FOR NOW (lack of capacity) // Protein cavity identification and automatic subpocket decomposition☆46Jul 23, 2023Updated 2 years ago
- A collection of *fold* tools☆305Aug 8, 2025Updated 10 months ago
- Code and resources for the EPSRC BioSimSpace project.☆78Sep 1, 2025Updated 9 months ago
- Jupyter widget to interactively view molecular structures and trajectories☆925Feb 2, 2026Updated 4 months ago
- Notebooks demonstrating how to do simple tasks related to free energy calculations.☆68Jun 12, 2026Updated last week
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- machine learning, molecular descriptor☆120Apr 10, 2023Updated 3 years ago
- This repository has been integrated in https://github.com/DeepRank/deeprank2☆147Nov 28, 2023Updated 2 years ago
- Open Drug Discovery Toolkit☆465Dec 13, 2022Updated 3 years ago
- Cloud-based molecular simulations for everyone☆492Jan 20, 2026Updated 4 months ago
- Collected scripts for Pymol☆528Mar 1, 2026Updated 3 months ago
- A comprehensive library for computational molecular biology☆958Jun 11, 2026Updated last week
- Full automation of relative protein-ligand binding free energy calculations in GROMACS☆46May 3, 2021Updated 5 years ago
- Calculation of interatomic interactions in molecular structures☆136Sep 3, 2024Updated last year
- Make valid molecular graphs!☆23Mar 8, 2024Updated 2 years ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Preforms De novo protein design using machine learning and PyRosetta to generate a novel protein structure☆52Mar 7, 2025Updated last year
- DENOPTIM is a software package for de novo design and virtual screening of functional molecules of any kind.☆39Updated this week
- The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy (ABFE) and relative binding free energy (RB…☆224Mar 4, 2026Updated 3 months ago
- ATOM3D: tasks on molecules in three dimensions☆319Mar 2, 2023Updated 3 years ago
- Python interface of cpptraj☆191Mar 6, 2026Updated 3 months ago
- EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein☆545Feb 19, 2025Updated last year
- Python interface for the RCSB search API.☆20Mar 20, 2024Updated 2 years ago