PaCS-Toolkit: Optimized software utilities for PaCS-MD and following analysis
☆29Dec 14, 2025Updated 10 months ago
Alternatives and similar repositories for PaCS-Toolkit
Users that are interested in PaCS-Toolkit are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- PaCS-Q is a Python toolkit designed to assist with Parallel Cascade Selection simulations (PaCS) for studying protein structural transiti…☆21Updated this week
- Tree Search Molecular Dynamics Simulation☆11Aug 25, 2019Updated 7 years ago
- ☆14Feb 18, 2025Updated last year
- ☆11Aug 24, 2025Updated last year
- Combs repo associated with Lu et al 2024 Science paper☆17Sep 21, 2025Updated last year
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- A versatile tool to investigate membrane☆11Dec 12, 2024Updated last year
- EnzyDock: Protein–Ligand Docking of Multiple Reactive States along a Reaction Coordinate in Enzymes☆18Sep 5, 2024Updated 2 years ago
- ☆26Mar 9, 2026Updated 7 months ago
- VMD Tcl language scripts of molecular dynamics modeling, analyzing, and visualization.☆11Apr 12, 2020Updated 6 years ago
- Small_molecule_binder_design_use_pseudocycles☆26Nov 19, 2024Updated last year
- Rapid generation of high-quality structure figures for publication with PyMOL-PUB☆99Oct 30, 2024Updated 2 years ago
- Random Acceleration Molecular Dynamics in GROMACS☆46Sep 7, 2026Updated 2 months ago
- Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) calculations in protein-protein and protein-ligand systems☆11Mar 30, 2022Updated 4 years ago
- (Windows) AMDock: Assisted molecular docking with AutoDock4 and AutoDockVina☆73Jul 7, 2026Updated 4 months 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.
- Introduction to cyclic peptide simulations and our group's protocols.☆18Sep 21, 2023Updated 3 years ago
- ☆10Jul 11, 2021Updated 5 years ago
- SubPEx (Sub-Pocket Explorer) is a tool to enhance ensemble (multiple-receptor/relaxed-complex) virtual screening. It uses weighted ensemb…☆18Jun 30, 2025Updated last year
- De novo design of small molecule binding sites into proteins☆11Apr 14, 2021Updated 5 years ago
- Alchemd is a Python-based CADD (Computer-Aided Drug Design) application specialized in free energy perturbation (FEP) calculations using …☆11May 26, 2026Updated 5 months ago
- Workshop - Analysis of Molecular Dynamics Simulation Using Python☆20Aug 14, 2020Updated 6 years ago
- A semi-automated force field converter for GROMACS. Enables users to easily convert a system between two all-atom force fields. Requires …☆18Aug 1, 2026Updated 3 months ago
- ☆23Oct 2, 2024Updated 2 years ago
- ☆12Sep 17, 2024Updated 2 years 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.
- A pocket volume analyzer for use in protein modeling.☆65Oct 2, 2022Updated 4 years ago
- Pairwise interaction segment activity coefficients, reference implementation in Python☆20Apr 27, 2024Updated 2 years ago
- This is a simple script to use [plip](https://github.com/pharmai/plip) to batch analysis of interactions between proteins and ligands tha…☆10Dec 23, 2020Updated 5 years ago
- ☆24Dec 14, 2025Updated 10 months ago
- ☆20Oct 3, 2024Updated 2 years ago
- Code for designing binders to flexible peptides with AlphaFold2 Hallucination☆30Dec 21, 2023Updated 2 years ago
- An application for configuring and running simulations with OpenMM☆84Oct 30, 2025Updated last year
- An automatic workflow to perform MM/GB(PB)SA calculations from force field building, and structure optimization to free energy calculatio…☆154Jan 13, 2026Updated 9 months ago
- ☆29May 5, 2025Updated last year
- Simple, predictable pricing with DigitalOcean hosting • AdAlways know what you'll pay with monthly caps and flat pricing. Enterprise-grade infrastructure trusted by 600k+ customers.
- The code for the QuickVina homepage.☆37Nov 7, 2022Updated 4 years ago
- Catalyst design for the Morita−Baylis−Hillman Reaction using a graph-based genetic algorithm☆11Jul 15, 2024Updated 2 years ago
- Deep learning AI for generating new molecules that bond to the COVID-19.☆12Sep 17, 2020Updated 6 years ago
- a library for massive analyses of internal voids in biomolecules and ligand transport through them☆10Aug 27, 2026Updated 2 months ago
- cp2k-2-deepmdkit (c2d): A comprehensive tool for converting cp2k output to DeepMD-kit input☆10Aug 19, 2024Updated 2 years ago
- Biobb (BioExcel building blocks) packages are Python building blocks that create new layer of compatibility and interoperability over pop…☆68Updated this week
- Utility for building inverse rotamer assemblies out of a Rosetta matcher/enzdes constraint file.☆31Mar 8, 2025Updated last year