PARENT: a parallel software suite for the calculation of configurational entropy in biomolecular systems
☆16Jan 20, 2022Updated 4 years ago
Alternatives and similar repositories for PARENT
Users that are interested in PARENT are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ☆15Jun 26, 2018Updated 8 years ago
- A scoring function model based on 3D convolutional neural network for protein-ligand binding affinity prediction.☆17Oct 8, 2021Updated 4 years ago
- ☆10Feb 18, 2020Updated 6 years ago
- A Python library for constructing polymer topologies and coordinates☆22Sep 23, 2025Updated 9 months ago
- Perform polymerization and crosslinking in MARTINI coarse-grained forcefield using GROMACS MD package☆30Jan 21, 2026Updated 6 months 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.
- Combines FRESEAN mode analysis of a protein (based on a CG representation) with enhanced sampling using metadynamics☆16May 7, 2026Updated 2 months ago
- Clustering of SES virtual probes for pocket generation and ranking via Isolation Forest☆14Mar 22, 2023Updated 3 years ago
- Robust and stable clustering of molecular dynamics simulation trajectories.☆20Sep 2, 2022Updated 3 years ago
- Entropy from PDB conformational ensembles☆13Mar 28, 2024Updated 2 years ago
- ☆13Sep 29, 2023Updated 2 years ago
- Generate Ramachandran plots for single PDB structure and as heatmap for MD trajectory☆11Apr 6, 2022Updated 4 years ago
- Generate coarse-grained molecular dynamics models from atomistic trajectories.☆68Nov 26, 2025Updated 7 months ago
- scripts for analyzing molecular dynamics trajectories using VMD☆40May 28, 2015Updated 11 years ago
- Geometric super-resolution for molecular geometries☆43Jun 15, 2022Updated 4 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Tools for coarse-grained molecular dynamics simulations using the SPICA force field☆13May 12, 2026Updated 2 months ago
- Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation te…☆19Oct 27, 2022Updated 3 years ago
- Funnel maker is a set of scripts that sets up funnel metadynamics simulations for protein-ligand binding with PLUMED and OpenMM.☆15Jan 3, 2026Updated 6 months ago
- Building and analyzing residue interaction networks with cofactors (includes tutorial).☆19Mar 31, 2021Updated 5 years ago
- An efficient approach to RMSD-Based HDBSCAN Clustering of long Molecular Dynamics☆18Sep 11, 2022Updated 3 years ago
- Advanced toolkit for binding free energy calculations☆36Sep 2, 2025Updated 10 months ago
- QM/MM Study Group☆15Jan 22, 2019Updated 7 years ago
- Package for reading, analysis and visualization of metadynamics HILLS☆41Nov 28, 2023Updated 2 years ago
- calculating RMSD between 2 conformers with different atom names☆13Jan 13, 2021Updated 5 years ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Software package for FEP☆23Mar 3, 2026Updated 4 months ago
- ☆16Apr 11, 2025Updated last year
- PaCS-Q is a Python toolkit designed to assist with Parallel Cascade Selection simulations (PaCS) for studying protein structural transiti…☆21Apr 30, 2026Updated 2 months ago
- Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations☆22Mar 13, 2018Updated 8 years ago
- Force field-inspired molecular representation learning model☆22Sep 26, 2023Updated 2 years ago
- A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison☆19Jun 6, 2023Updated 3 years ago
- Discontinuous Molecular Dynamics (DMD) Simulation Package☆16Jun 8, 2026Updated last month
- GridMAT-MD membrane analysis program☆26Sep 15, 2018Updated 7 years ago
- Protein Sequence Evolutionary Information Language Model☆14Oct 5, 2023Updated 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.
- OpenFF NAGL☆22Updated this week
- Analysis framework of dissipation-corrected targeted molecular dynamics (dcTMD) simulations.☆17Jul 13, 2026Updated last week
- MLP training for molecular systems☆60Jul 8, 2026Updated last week
- Sample code from Allen & Tildesley's Computer Simulation of Liquids, 1st Ed. See https://github.com/Allen-Tildesley/examples for moderni…☆18Sep 10, 2017Updated 8 years ago
- Optimization tool for calibrating coarse-grained force fields of lipids, relying on the simultaneous usage of reference AA trajectories (…☆10Jun 6, 2023Updated 3 years ago
- Ramachandran plotting tool☆21May 26, 2026Updated last month
- AlphaFlow Reinforcement Learning☆10Apr 13, 2023Updated 3 years ago