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Lore is a next-generation, open source version control system
Distance-based Analysis of DAta-manifolds in python
An interoperable Python framework for biomolecular simulation.
pyenv for Windows. pyenv is a simple python version management tool. It lets you easily switch between multiple versions of Python. It's simple, unobtrusive, and follows the UNIX tradition of singl…
DockQ is a single continuous quality measure for Protein, Nucleic Acids and Small Molecule Docking Models
A workflow language for data-driven computational pipelines
package to generate relative rotational positions and orientations of two molecular structures
Hierarchical Generation of Molecular Graphs using Structural Motifs
Application to assign secondary structure to proteins
PandaDock: Physics based Molecular Docking with GNN Scoring
WESTPA: The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis
Weighted Ensemble simulation framework in Python
Adds NME and ACE caps to protein pdbs based on chain number/id
s3path is a pathlib extension for AWS S3 Service
Parsers for Molecular Dynamics related file types
PENSA - a collection of python methods for exploratory analysis and comparison of biomolecular conformational ensembles.
Deep universal probabilistic programming with Python and PyTorch
A geometric flow matching model for generative protein-ligand docking and affinity prediction. (ISMB 2025)
Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology
Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Schake, Bolz, et al. (2025), https://doi.org/10.1093/nar/gkaf361
MDANCE: Hyper-efficient tools to process molecular dynamics simulations.
A python script to perform QM/MM calculation.
fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and…
A Toolbox for Post-Processing Quantum Chemical Wavefunction Data