Python code to run Thermal Titration Molecular Dynamics (TTMD) simulations
☆21Feb 25, 2026Updated 4 months ago
Alternatives and similar repositories for TTMD
Users that are interested in TTMD are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Input files and binding free energy values from our benchmark with QuantumBind-RBFE☆16Apr 16, 2025Updated last year
- MCP server for Rosetta/PyRosetta and Biotite: give your AI coding agent expert-level knowledge of protein modeling and design - ask naive…☆16Apr 5, 2026Updated 3 months ago
- P2DFlow: A Protein Ensemble Generative Model with SE(3) Flow Matching☆43May 22, 2025Updated last year
- A geometric flow matching model for generative protein-ligand docking and affinity prediction. (ISMB 2025)☆141Sep 3, 2025Updated 10 months ago
- Genetic algorithm to convert 3D-RISM solvent densities to explicit water molecules in binding pockets☆13Dec 19, 2017Updated 8 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.
- Code for the paper "Learning to engineer protein flexibility".☆22Mar 24, 2026Updated 3 months ago
- Interface to OpenMM for easy setup of molecular dynamic simulations of protein-ligand complexes☆174May 22, 2026Updated last month
- Display PackedPose objects, Pose objects, or PDB files within a Jupyter notebook and Google Colab☆11Jun 28, 2026Updated 3 weeks ago
- Re-scoring a set of docked ligands with off-the-shelf algorithms to assess utility in virtual screening☆11Oct 13, 2021Updated 4 years ago
- Automated Adaptive Absolute alchemical Free Energy calculator☆123May 1, 2026Updated 2 months ago
- Implementation of SCINS☆17Nov 6, 2024Updated last year
- Feynman-Kac steering for controllable protein diffusion☆37Jan 14, 2026Updated 6 months ago
- A snakemake-based workflow for FEP and MM(PB/GB)SA calculations with GROMACS☆169May 9, 2026Updated 2 months ago
- A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD☆16Apr 3, 2026Updated 3 months ago
- 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.
- ☆27Apr 26, 2023Updated 3 years ago
- Physics-Guided All-Atom Diffusion Model for Accurate Protein-Ligand Complex Prediction☆91Oct 6, 2025Updated 9 months ago
- Tool to predict water molecules placement and energy in ligand binding sites☆37Sep 16, 2025Updated 10 months ago
- Plugin for folding sequences directly in PyMOL☆119Aug 4, 2025Updated 11 months ago
- An open-source platform for developing protein models beyond AlphaFold.☆11Jul 15, 2025Updated last year
- Simulation-Enabled Estimation of Kinetic Rates - Version 2☆35Dec 10, 2025Updated 7 months ago
- SableBind is an open-source framework dedicated to predicting protein-ligand binding affinity☆13Feb 6, 2025Updated last year
- ☆13May 18, 2026Updated 2 months ago
- ☆17Sep 26, 2025Updated 9 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.
- Tools for coarse-grained molecular dynamics simulations using the SPICA force field☆13May 12, 2026Updated 2 months ago
- Free Parametrization for Small Molecules☆66Jun 30, 2026Updated 3 weeks ago
- Density based object completion over PBC.☆33Apr 23, 2026Updated 2 months ago
- MAGPIE☆17May 5, 2024Updated 2 years ago
- Neural Iterative Selection-Expansion using LigandMPNN/LASErMPNN and Boltz-2x☆59Jul 14, 2026Updated last week
- ☆29Jul 28, 2023Updated 2 years ago
- pyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the Univer…☆76Jun 30, 2026Updated 2 weeks ago
- ☆15Jun 3, 2025Updated last year
- Solvation Structure and Thermodynamic Mapping☆42Dec 17, 2025Updated 7 months ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Repo for the publication titled: "Key Interaction Networks: Identifying Evolutionarily Conserved Non-Covalent Interaction Networks Across…☆18Nov 14, 2023Updated 2 years ago
- ☆68Apr 28, 2025Updated last year
- Notebooks demonstrating how to do simple tasks related to free energy calculations.☆68Jul 7, 2026Updated 2 weeks ago
- gpu implementation mopac☆16Oct 11, 2025Updated 9 months ago
- ☆79May 4, 2026Updated 2 months ago
- ☆16Dec 24, 2016Updated 9 years ago
- Histidine Protonation State Optimizer for setting up MD simulations based on semi-empirical QM resonance☆20Mar 6, 2026Updated 4 months ago