Python code to run Thermal Titration Molecular Dynamics (TTMD) simulations
☆22Feb 25, 2026Updated 7 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:
- Automated Adaptive Absolute alchemical Free Energy calculator☆132Updated this week
- Input files and binding free energy values from our benchmark with QuantumBind-RBFE☆19Apr 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…☆19Apr 5, 2026Updated 6 months ago
- P2DFlow: A Protein Ensemble Generative Model with SE(3) Flow Matching☆46May 22, 2025Updated last year
- Genetic algorithm to convert 3D-RISM solvent densities to explicit water molecules in binding pockets☆13Dec 19, 2017Updated 8 years ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Code for the paper "Learning to engineer protein flexibility".☆22Mar 24, 2026Updated 6 months ago
- Interface to OpenMM for easy setup of molecular dynamic simulations of protein-ligand complexes☆177Sep 7, 2026Updated last month
- Display PackedPose objects, Pose objects, or PDB files within a Jupyter notebook and Google Colab☆11Aug 29, 2026Updated last month
- Re-scoring a set of docked ligands with off-the-shelf algorithms to assess utility in virtual screening☆11Oct 13, 2021Updated 4 years ago
- A tutorials suite for BioSimSpace.☆37Oct 22, 2025Updated 11 months ago
- Feynman-Kac steering for controllable protein diffusion☆39Aug 16, 2026Updated last month
- A snakemake-based workflow for FEP and MM(PB/GB)SA calculations with GROMACS☆168May 9, 2026Updated 5 months ago
- ☆27Apr 26, 2023Updated 3 years ago
- Physics-Guided All-Atom Diffusion Model for Accurate Protein-Ligand Complex Prediction☆94Sep 28, 2026Updated last week
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- A geometric flow matching model for generative protein-ligand docking and affinity prediction. (ISMB 2025)☆146Sep 7, 2026Updated last month
- ☆15Apr 17, 2025Updated last year
- Plugin for folding sequences directly in PyMOL☆119Aug 4, 2025Updated last year
- An open-source platform for developing protein models beyond AlphaFold.☆11Jul 15, 2025Updated last year
- Simulation-Enabled Estimation of Kinetic Rates - Version 2☆36Dec 10, 2025Updated 9 months ago
- ☆13Updated this week
- SableBind is an open-source framework dedicated to predicting protein-ligand binding affinity☆13Feb 6, 2025Updated last year
- ☆17Sep 26, 2025Updated last year
- Tools for coarse-grained molecular dynamics simulations using the SPICA force field☆13May 12, 2026Updated 4 months ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Implementation of SCINS☆17Nov 6, 2024Updated last year
- Free Parametrization for Small Molecules☆66Jun 30, 2026Updated 3 months ago
- Knowledge-Guided Diffusion Model for 3D Ligand-Pharmacophore Mapping☆52Sep 27, 2026Updated last week
- Density based object completion over PBC.☆33Apr 23, 2026Updated 5 months ago
- A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD☆17Apr 3, 2026Updated 6 months ago
- MAGPIE☆17May 5, 2024Updated 2 years ago
- Neural Iterative Selection-Expansion using LigandMPNN/LASErMPNN and Boltz-2x☆73Aug 11, 2026Updated last month
- ☆29Jul 28, 2023Updated 3 years ago
- pyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the Univer…☆76Jun 30, 2026Updated 3 months ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- ☆17Jun 3, 2025Updated last year
- Solvation Structure and Thermodynamic Mapping☆42Dec 17, 2025Updated 9 months ago
- 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.☆70Updated this week
- Tool to predict water molecules placement and energy in ligand binding sites☆40Sep 16, 2025Updated last year
- ☆80May 4, 2026Updated 5 months ago