A repository containing the build steps for the ccpbiosim workshop on Clustering.
☆11Oct 27, 2026Updated last week
Alternatives and similar repositories for clustering-workshop
Users that are interested in clustering-workshop are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ☆17Jul 28, 2022Updated 4 years ago
- ☆23Jul 29, 2026Updated 3 months ago
- Workshop on the preparation, execution, and analysis of protein molecular dynamics simulations☆13May 7, 2025Updated last year
- Automatically prepare structures from the PDB for molecular dynamics simulation☆15Updated this week
- ☆23Dec 11, 2024Updated last year
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆44Apr 27, 2026Updated 6 months ago
- A tool for the analysis of pathways sampled in molecular dynamics simulations based on Self-Organizing Maps (SOM)☆10Jan 26, 2022Updated 4 years ago
- A tool for setting up free energy simulations.☆37Oct 20, 2022Updated 4 years ago
- Dynamics PyMOL Plugin☆49Apr 19, 2024Updated 2 years ago
- To run metadynamics simulations using openMM (based on Peter Eastman's script)☆13Mar 18, 2019Updated 7 years ago
- A repository containing the build steps for the ccpbiosim workshop on QM/MM☆70Oct 27, 2026Updated last week
- Molecular Dynamics Sub Sampler☆10Jul 24, 2024Updated 2 years ago
- Jupyter Notebook showing how to plot FES, histograms and time-series data using Matplotlib.☆13Dec 21, 2020Updated 5 years ago
- BioMetAll is a command line application to allow the identification of metal-binding sites in proteins from backbone preorganization.☆13Jun 9, 2026Updated 4 months ago
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- Codes to use funnel-metadynamics and funnel metadynamics automated protocol☆31Dec 19, 2021Updated 4 years ago
- ☆35Aug 28, 2026Updated 2 months ago
- Parallelizable Gaussian Accelerated Molecular Dynamics☆11Mar 20, 2026Updated 7 months ago
- A repository of the analysis and simulation tools for biomolecular modeling, simulations and drug discovery☆13Mar 7, 2025Updated last year
- Conformer-Rotamer Ensemble Sampling Tool based on the xtb Semiempirical Extended Tight-Binding Program Package☆38Jun 16, 2026Updated 4 months ago
- A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD☆17Apr 3, 2026Updated 7 months ago
- This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.☆65Dec 17, 2025Updated 10 months ago
- PyEMMA Jupyter Notebooks☆13Jan 28, 2021Updated 5 years ago
- Materials, issues and things for the 2018 Workshop and Hackathon☆15Jul 25, 2025Updated last year
- 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.
- Funnel maker is a set of scripts that sets up funnel metadynamics simulations for protein-ligand binding with PLUMED and OpenMM.☆15Jan 3, 2026Updated 10 months ago
- Tutorials on doing AMBER based Metadynamics and Gaussian Accelerated MD (GaMD)☆13Dec 1, 2025Updated 11 months ago
- ☆14Sep 18, 2023Updated 3 years ago
- References, presentations and other resources☆15Oct 31, 2023Updated 3 years ago
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆20Oct 29, 2026Updated last week
- ☆15Jun 11, 2024Updated 2 years ago
- ☆17Jun 27, 2026Updated 4 months ago
- Protocols and tools to run (automated) atomistic simulations of enzyme-ligand systems☆15Jun 15, 2019Updated 7 years ago
- ☆66Jul 25, 2025Updated last year
- 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.
- NAMD QM/MM Tutorial on Free Energy Profile of Reaction Mechanisms☆17Sep 14, 2018Updated 8 years ago
- Fraction of Common Contacts Clustering Algorithm for Protein Structures☆28Aug 12, 2021Updated 5 years ago
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆186Jul 28, 2026Updated 3 months ago
- Protocol to redesign enzyme sequences for stability and expression followed in Krasnow et. al. 2025 (). Developed using ProteinMPNN (Daup…☆21May 11, 2026Updated 5 months ago
- Full automation of relative protein-ligand binding free energy calculations in GROMACS☆47May 3, 2021Updated 5 years ago
- MSMD (mixed-solvent molecular dynamics) engine and analysis tools☆18Apr 16, 2026Updated 6 months ago
- Robust and stable clustering of molecular dynamics simulation trajectories.☆20Sep 2, 2022Updated 4 years ago