tubiana / TTClustView external linksLinks
clusterize molecular dynamic trajectories (amber, gromacs, charmm, namd, pdb...)
☆128Apr 25, 2024Updated last year
Alternatives and similar repositories for TTClust
Users that are interested in TTClust are comparing it to the libraries listed below
Sorting:
- Robust and stable clustering of molecular dynamics simulation trajectories.☆19Sep 2, 2022Updated 3 years ago
- We provide a set of scripts to calculate native contacts from a MD. Native contacts are determined according to the overlap and rCSU appr…☆16Jul 2, 2024Updated last year
- MMTSB Tool Set☆33Jan 26, 2026Updated 3 weeks ago
- Biomolecular simulation trajectory/data analysis.☆163Feb 5, 2026Updated last week
- gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.☆295Dec 8, 2025Updated 2 months ago
- A collection of scripts which I have developed to use GROMACS, for both compute clusters and post-simulation analysis.☆11Jul 15, 2014Updated 11 years ago
- Automatic gromacs protocol from preparation to production with ligand parametrization through☆80Apr 6, 2025Updated 10 months ago
- A python script to prepare GROMACS input files using INTERFACE forcefield☆27Mar 22, 2022Updated 3 years ago
- PDBFixer fixes problems in PDB files☆622Oct 30, 2025Updated 3 months ago
- Parameter/topology editor and molecular simulator☆448Jan 12, 2026Updated last month
- Membrane protein builder and parameterizer☆19Sep 1, 2024Updated last year
- DeltaVina scoring function☆42Apr 7, 2017Updated 8 years ago
- Biobb (BioExcel building blocks) packages are Python building blocks that create new layer of compatibility and interoperability over pop…☆64Dec 22, 2025Updated last month
- Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…☆92Jul 16, 2025Updated 7 months ago
- scripts for analyzing molecular dynamics trajectories using VMD☆39May 28, 2015Updated 10 years ago
- A toolkit for predicting the binding mode of small molecules interacting with proteins based on interfacial rigidification, as assessed b…☆10Nov 22, 2016Updated 9 years ago
- Solvent network analysis. Hop is a python package based on MDAnalysis to analyze solvation dynamics.☆15Sep 20, 2018Updated 7 years ago
- example demonstrating a free energy estimation starting from OFF and OpenMM☆12Oct 21, 2020Updated 5 years ago
- Analysis of non-covalent interactions in MD trajectories☆66Jan 3, 2025Updated last year
- a VMD plugin for binding affinity prediction using end-point free energy methods☆28Apr 23, 2016Updated 9 years ago
- Cloud GPU supported NAMD3-based binding free energy difference between two small molecules against the same protein target. This is prob…☆28Nov 2, 2025Updated 3 months ago
- How to analyze molecular dynamics data with PyEMMA☆83May 29, 2019Updated 6 years ago
- a python package for the interfacial analysis of molecular simulations☆94Feb 8, 2026Updated last week
- Some collected tools for molecular simulation pipelines☆43Aug 18, 2018Updated 7 years ago
- The App Store for VMD extensions.☆14Jan 14, 2023Updated 3 years ago
- Codes to use funnel-metadynamics and funnel metadynamics automated protocol☆31Dec 19, 2021Updated 4 years ago
- Examples for use of YANK - getyank.org☆12Sep 20, 2021Updated 4 years ago
- A Python package to calculate, visualize and analyze correlation maps of proteins.☆44Sep 3, 2025Updated 5 months ago
- Parallelized Open Babel & Autodock suite Pipeline☆24Mar 15, 2018Updated 7 years ago
- Main repository for METAGUI3☆20Jun 19, 2021Updated 4 years ago
- Python interface of cpptraj☆188Jan 20, 2026Updated 3 weeks ago
- Features Based Conformational Clustering of MD trajectories. See details at:☆10Nov 20, 2025Updated 2 months ago
- Calculation of water/solvent partition coefficients with Gromacs.☆29Oct 14, 2024Updated last year
- (Linux and macOS) AMDock: Assisted molecular docking with AutoDock4 and AutoDockVina☆74Aug 3, 2023Updated 2 years ago
- Cloud-based molecular simulations for everyone☆471Jan 20, 2026Updated 3 weeks ago
- PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.☆336Updated this week
- Repository of the data for PLUMED Masterclass 22.3☆14Jul 10, 2024Updated last year
- Adaptive landscape flattening scripts for MSLD☆17Feb 11, 2026Updated last week
- ☆18Oct 30, 2023Updated 2 years ago