Python package built around protein structure and dynamics. OpenBabel-inspired objects.
☆37May 23, 2025Updated 9 months ago
Alternatives and similar repositories for PACKMAN
Users that are interested in PACKMAN are comparing it to the libraries listed below
Sorting:
- QM/MM interfacing in Python☆10Feb 12, 2019Updated 7 years ago
- Pocket to Concavity is a tool for refinement of Protein-Ligand binding site shape from alpha-spheres☆16Oct 2, 2024Updated last year
- PyMOL Plugin for displaying polar contacts☆18Mar 11, 2019Updated 6 years ago
- An experimental package for deep learning for molecular docking☆21Mar 21, 2020Updated 5 years ago
- Adaptive string method implementation in AmberTools23 and Amber22☆14Jan 7, 2025Updated last year
- ☆14Dec 18, 2024Updated last year
- Entropy from PDB conformational ensembles☆13Mar 28, 2024Updated last year
- A python implementation of pdb2oniom for QM/MM (ONIOM) calculations☆10Oct 2, 2025Updated 5 months ago
- Weighted Ensemble Data Analysis and Plotting☆26Dec 11, 2025Updated 2 months ago
- Scripts to interface TorchANI NNP with NAMD☆32Aug 1, 2023Updated 2 years ago
- Ligand-Receptor docking with AutoDock Vina☆12Mar 21, 2024Updated last year
- Implementation of multi-output conformal regression methods☆13Sep 23, 2025Updated 5 months ago
- Predict the boundary of transcript start and end from RNA-seq reads alignment☆11Feb 13, 2017Updated 9 years ago
- Mol* Volumes and Segmentations Extension☆12Mar 16, 2025Updated 11 months ago
- Dock Multiple Ligands with AutoDock Vina with one Command☆11Jan 10, 2018Updated 8 years ago
- Map genetic variants and protein positions to protein interfaces in 3D☆13Sep 22, 2023Updated 2 years ago
- Protein representation and design under a single training scheme☆24Updated this week
- Normal Mode Analysis for Macromolecules☆18Apr 1, 2017Updated 8 years ago
- PLM-interact: extending protein language models to predict protein-protein interactions.☆61Aug 29, 2025Updated 6 months ago
- TUnA: Transformer-based Uncertainty Aware model for PPI Prediction☆14Dec 21, 2025Updated 2 months ago
- Collection of tools for running MD, QM, and QM/MM calculations☆20Sep 27, 2025Updated 5 months ago
- Automatic Retrieval and ClusTering of Interfaces in Complexes from 3D structural information☆32Jan 22, 2026Updated last month
- Simulation-Enabled Estimation of Kinetic Rates - Version 2☆35Dec 10, 2025Updated 2 months ago
- Protein Structure Archiver☆14Sep 10, 2025Updated 5 months ago
- Automated construction of protein chimeras and their analysis.☆14Sep 29, 2023Updated 2 years ago
- NAMD's psfgen + Python improvements☆16Sep 1, 2024Updated last year
- ☆18Oct 30, 2023Updated 2 years ago
- A collection of tutorials for the python implementation of Dynamical Network Analysis☆15Aug 6, 2025Updated 6 months ago
- Protocols and tools to run (automated) atomistic simulations of enzyme-ligand systems☆15Jun 15, 2019Updated 6 years ago
- WESTPA: The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis☆210Feb 23, 2026Updated last week
- We provide a set of scripts to calculate native contacts from a MD. Native contacts are determined according to the overlap and rCSU appr…☆16Jul 2, 2024Updated last year
- a deep learning framework for essential protein prediction☆13Mar 24, 2023Updated 2 years ago
- ☆17Jun 27, 2025Updated 8 months ago
- ☆35Oct 14, 2024Updated last year
- WebGL based molecular viewer☆36Feb 13, 2026Updated 2 weeks ago
- QMCube: An all-purpose suite for multiscale QM/MM calculations☆13Dec 13, 2024Updated last year
- Running a molecular simulation with the polarizable force field in LAMMPS☆20Jan 9, 2023Updated 3 years ago
- A collection of molecular modelling tools for UCSF Chimera☆17Mar 26, 2019Updated 6 years ago
- This repo contains the collection of codes to find designer interfacial mutations☆17Sep 4, 2023Updated 2 years ago