52 dependents
| Package | Description | Downloads/month |
|---|---|---|
| PDBFixer fixes problems in PDB files | 13K | |
| Generate realistic PDB files with mixed secondary structures for testing, educat... | 4K | |
| A collection of molecular optimisers and property calculators for use with stk. | 4K | |
| All-in-one protein-ligand docking package for Windows with bundled tools | 2K | |
| Log MD trajectories. | 2K | |
| PDBFixer fixes problems in PDB files. This repository is used to release to PyPI | 2K | |
| Scripts for MD Analysis | 2K | |
| Sandbox for Computational Protein Design | 2K | |
| Hit Interaction Profiling and Procurement Optimisation | 1K | |
| A genomewide multiscale energy minimization model. | 1K | |
| 1K | ||
| Python toolkit for the analysis of protein protonation states and residue-level ... | 993 | |
| Predict per-residue Fdewet using SASA + MPNN | 959 | |
| 883 | ||
| MCP server for gget bioinformatics library | 859 | |
| A software that simulates the dynamics of DNA replication by following a sofisti... | 734 | |
| Lightweight antibody structure prediction tool (arXiv:2507.09054) | 665 | |
| ACEMD is the next generation molecular dynamic simulation software | 645 | |
| 639 | ||
| Compute possible interaction between molecules. | 633 | |
| Cryo-EM Ensemble Optimization using JAX and OpenMM for Molecular Dynamics simula... | 621 | |
| Useful Collective Variables for OpenMM | 559 | |
| An energy-based stochastic model of loop extrusion in chromatin. | 492 | |
| MCP server for FutureHouse platform integration | 420 | |
| Fork of pdbfixer (https://github.com/openmm/pdbfixer) to be able to pip install ... | 384 | |
| Polymer-Oriented LibrarY of Monomer-Expression Rules and In-silico Synthesis Too... | 348 | |
| https://pypi.org/project/pmarlo/ | 330 | |
| 325 | ||
| Umbrella monorepo for the Neoralab OpenFF stack | 324 | |
| A drop-in replacement for Rosetta Relax | 289 | |
| MCP server for Edison Scientific platform integration (former FutureHouse) | 282 | |
| High level API for using machine learning models in OpenMM simulations | 281 | |
| neoralab fork: PDBFixer fixes problems in PDB files | 275 | |
| A Toolset For Molecular Dynamics | 272 | |
| High-Throughput Cross-Docking (NxM) — cross-dock massive ligand libraries agains... | 263 | |
| ProteusAI is a library for the machine learning driven engineering of proteins. ... | 217 | |
| An advanced neural network framework with interpretability, generalization, robu... | 214 | |
| Unified RNA Analysis Toolkit - ML-powered RNA sequence analysis and structure pr... | 205 | |
| docking is all you need... | 204 | |
| Hit Interaction Profiling and Procurement Optimisation | 158 | |
| MCP server for gget bioinformatics library | 157 | |
| A Python package for building and simulating carbohydrate structures. | 151 | |
| A Python package for preparing proteins and ligands for molecular docking | 126 | |
| Calculates single residue frustration, and mutational frustration of proteins. | 120 | |
| Molecular Machine Learning for Chemical Applications - A comprehensive Python pa... | 117 | |
| Simple program to prepare PDb files using combination of PDBFixer, RDkit and Ope... | 108 | |
| Extended Phase-Space Simulations with OpenMM | 100 | |
| OpenMM Setup: User interface for preparing and running OpenMM simulations | 97 | |
| A toolkit for data-driven force field design based on binary-encoded SMARTS | 83 | |
| CLI tools for quick protein structure cleanup and optimization with OpenMM. | 80 |
