PaCS-Q is a Python toolkit designed to assist with Parallel Cascade Selection simulations (PaCS) for studying protein structural transitions in MD and QM/MM MD level.
☆21Apr 30, 2026Updated 3 months ago
Alternatives and similar repositories for PaCS-Q
Users that are interested in PaCS-Q are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ☆13Sep 29, 2023Updated 2 years ago
- PaCS-Toolkit: Optimized software utilities for PaCS-MD and following analysis☆28Dec 14, 2025Updated 7 months ago
- pyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the Univer…☆76Jun 30, 2026Updated last month
- Input files and binding free energy values from our benchmark with QuantumBind-RBFE☆16Apr 16, 2025Updated last year
- Combines FRESEAN mode analysis of a protein (based on a CG representation) with enhanced sampling using metadynamics☆17May 7, 2026Updated 3 months ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Python based Graphical User Interface for generating input files for and running molecular dynamic simulation.☆10Aug 27, 2024Updated last year
- ☆15May 18, 2026Updated 2 months ago
- ☆40Jul 17, 2024Updated 2 years ago
- A step-by-step tutorial to run Molecular Dynamics Simulations with enhanced sampling of a pepitide using PLUMED implemented in GROMACS to…☆16Mar 4, 2024Updated 2 years ago
- A python implementation of pdb2oniom for QM/MM (ONIOM) calculations☆12Oct 2, 2025Updated 10 months ago
- Adaptive string method implementation in AmberTools23 and Amber22☆15Jan 7, 2025Updated last year
- MLP training for molecular systems☆61Updated this week
- Clustering of SES virtual probes for pocket generation and ranking via Isolation Forest☆14Mar 22, 2023Updated 3 years ago
- A program for the conformational search in flexible acyclic molecules☆11Jul 12, 2022Updated 4 years ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- Funnel maker is a set of scripts that sets up funnel metadynamics simulations for protein-ligand binding with PLUMED and OpenMM.☆15Jan 3, 2026Updated 7 months ago
- CHEM331 - Physical Chemistry I☆11Dec 4, 2017Updated 8 years ago
- Utility scripts to generate and evaluate parametrically guided beta barrel protein backbone structures.☆13Nov 14, 2025Updated 8 months ago
- a unified interface for molecular harmonic vibrational frequency calculations☆34May 15, 2026Updated 2 months ago
- A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD☆16Apr 3, 2026Updated 4 months ago
- ☆37Jun 10, 2025Updated last year
- The pDynamo molecular modeling and simulation program☆49Nov 24, 2025Updated 8 months ago
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆43Apr 27, 2026Updated 3 months ago
- Protocols and tools to run (automated) atomistic simulations of enzyme-ligand systems☆15Jun 15, 2019Updated 7 years ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- 𝛂Charges: A tool for the quick calculation of partial atomic charges for protein structures from AlphaFold DB☆12Dec 16, 2025Updated 7 months ago
- ☆10Oct 31, 2025Updated 9 months ago
- Tinker-GPU: Next Generation of Tinker with GPU Support☆57Updated this week
- ☆22Jul 14, 2023Updated 3 years ago
- ☆20Nov 10, 2021Updated 4 years ago
- Fully automated high-throughput MD pipeline☆105Jul 23, 2026Updated 2 weeks ago
- OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method☆172Aug 2, 2026Updated last week
- PARENT: a parallel software suite for the calculation of configurational entropy in biomolecular systems☆16Jan 20, 2022Updated 4 years ago
- ☆90Nov 18, 2025Updated 8 months 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.
- Open-source protein-based pharmacophore modeling software☆42Feb 15, 2025Updated last year
- Source code for the reproduction of RibbonFold paper.☆12May 10, 2025Updated last year
- Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.☆26Oct 18, 2019Updated 6 years ago
- ☆16Apr 11, 2025Updated last year
- ☆35Feb 4, 2026Updated 6 months ago
- Boltzmann-ranked alternative protein conformations from reduced-MSA AlphaFold2☆63Updated this week
- Homomer symmetry prediction from protein sequence☆46Mar 13, 2025Updated last year