MM/PBSA binding free energy calculation
☆22May 31, 2024Updated 2 years ago
Alternatives and similar repositories for gmxpbsa
Users that are interested in gmxpbsa are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- a VMD plugin for binding affinity prediction using end-point free energy methods☆30Apr 23, 2016Updated 10 years ago
- An efficient approach to RMSD-Based HDBSCAN Clustering of long Molecular Dynamics☆18Sep 11, 2022Updated 4 years ago
- Danny Ma's 8 Week SQL Challenge Best Solutions on the Internet☆17Sep 20, 2024Updated 2 years ago
- gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.☆333Oct 24, 2026Updated 2 weeks ago
- MM-PBSA method for GROMACS. For full description, please visit homepage:☆70Jun 1, 2025Updated last year
- 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.
- ☆12Jul 30, 2019Updated 7 years ago
- Jupyter Notebook showing how to plot FES, histograms and time-series data using Matplotlib.☆13Dec 21, 2020Updated 5 years ago
- Clustering tool for biomolecular structural ensembles and data in general.☆10Aug 24, 2020Updated 6 years ago
- Extract ligand binding sites from PDB. Match the binding sites to de novo scaffolds.☆13Dec 29, 2020Updated 5 years ago
- PyMOL plugin to import Alphafold2 models hosted by EMBL, based on fetch-functionality☆24May 12, 2026Updated 5 months ago
- TPepPro: a deep learning model for predicting peptide-protein interactions☆15Jun 25, 2024Updated 2 years ago
- Perform operations on chemical structures using Python.☆13Mar 19, 2026Updated 7 months ago
- Python script to perform fingerprinting and calculate Tanimoto similarities on multiple compounds.☆22Mar 29, 2025Updated last year
- Generate and perturb protein structural ensembles using the ExProSE algorithm☆24Oct 23, 2024Updated 2 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.
- Yasara plugins for Gromacs users☆35Jan 8, 2024Updated 2 years ago
- Some GROMACS tutorials using methane and water☆16Dec 7, 2016Updated 9 years ago
- ☆12Jan 15, 2016Updated 10 years ago
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆69Apr 16, 2021Updated 5 years ago
- Analysing Sequence Activity Relationships (SARs) of protein sequences and their mutants using Machine Learning.☆10Jul 25, 2026Updated 3 months ago
- Python script that receives a molecular dynamics or Monte Carlo trajectory and performs agglomerative clustering to classify similar stru…☆30Sep 28, 2026Updated last month
- Histidine Protonation State Optimizer for setting up MD simulations based on semi-empirical QM resonance☆20Mar 6, 2026Updated 8 months ago
- Web application for protein-ligand binding sites analysis and visualization☆20Aug 22, 2026Updated 2 months ago
- Algorithm for identifying hydrogen bond networks in CG proteins to implement Go-like Martini 3 models☆17Oct 25, 2024Updated 2 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.
- ☆13Jul 11, 2026Updated 3 months ago
- Coarse grain to atomistic molecular coordinate and topology converter☆16Mar 13, 2025Updated last year
- ☆12Mar 31, 2023Updated 3 years ago
- OFFICIAL: AnteChamber PYthon Parser interfacE☆266Updated this week
- Tool suite for analysing molecular dynamics trajectories using network analysis and PRS☆55May 30, 2025Updated last year
- OCEAN - Optimized Cross rEActivity estimatioN☆12Apr 29, 2020Updated 6 years ago
- Lightweight induced fit docking☆22May 22, 2023Updated 3 years ago
- ☆23Dec 11, 2024Updated last year
- Computational Chemistry Workflows☆57Jul 19, 2022Updated 4 years ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- clusterize molecular dynamic trajectories (amber, gromacs, charmm, namd, pdb...)☆135Apr 25, 2024Updated 2 years ago
- Tutorial for the usage of the dcTMD approach and Langevin simulations employing the trypsin-benzamidine complex as example.☆11Jul 15, 2024Updated 2 years ago
- Building and analyzing residue interaction networks with cofactors (includes tutorial).☆19Mar 31, 2021Updated 5 years ago
- Random Acceleration Molecular Dynamics in GROMACS☆46Sep 7, 2026Updated 2 months ago
- Input files for GROMACS tutorials written for the Journal of Physical Chemistry B☆27Jul 21, 2024Updated 2 years ago
- Dock Multiple Ligands with AutoDock Vina with one Command☆11Jan 10, 2018Updated 8 years ago
- Example files for Colvars module: https://github.com/Colvars/colvars☆14Dec 7, 2021Updated 4 years ago