Python code to run Thermal Titration Molecular Dynamics (TTMD) simulations
☆20Updated this week
Alternatives and similar repositories for TTMD
Users that are interested in TTMD are comparing it to the libraries listed below
Sorting:
- Neural Iterative Selection-Expansion using LigandMPNN/LASErMPNN and Boltz-2x☆31Feb 12, 2026Updated 2 weeks ago
- Input files and binding free energy values from our benchmark with QuantumBind-RBFE☆16Apr 16, 2025Updated 10 months ago
- Protein design and sculpting using Rosetta and Deep learning methods (RFDiff and Alphafold2)☆49Feb 20, 2026Updated last week
- All-Atom (Including Hydrogen!) Ligand-Conditioned Protein Sequence Design & Sidechain Packing GNN☆27Feb 18, 2026Updated last week
- A geometric flow matching model for generative protein-ligand docking and affinity prediction. (ISMB 2025)☆126Sep 3, 2025Updated 5 months ago
- ReaSyn is a model for predicting a molecule's synthesis pathway, reaction steps from building blocks to final product(s), using an encode…☆77Jan 11, 2026Updated last month
- P2DFlow: A Protein Ensemble Generative Model with SE(3) Flow Matching☆44May 22, 2025Updated 9 months ago
- Code for the paper "Learning to engineer protein flexibility".☆22Jan 21, 2026Updated last month
- Physics-Guided All-Atom Diffusion Model for Accurate Protein-Ligand Complex Prediction☆87Oct 6, 2025Updated 4 months ago
- ParametrizANI - Fast, Accurate and Free Dihedral Parametrization in the Cloud with TorchANI☆22Jul 28, 2025Updated 7 months ago
- AbBFN2: A flexible antibody foundation model based on Bayesian Flow Networks☆37Jun 4, 2025Updated 8 months ago
- Automated Adaptive Absolute alchemical Free Energy calculator☆114Feb 9, 2026Updated 2 weeks ago
- Display PackedPose objects, Pose objects, or PDB files within a Jupyter notebook and Google Colab☆11Oct 16, 2022Updated 3 years ago
- ☆46Nov 19, 2025Updated 3 months ago
- SableBind is an open-source framework dedicated to predicting protein-ligand binding affinity☆13Feb 6, 2025Updated last year
- ESMDynamic repo☆22Updated this week
- A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD☆15Mar 20, 2025Updated 11 months ago
- ☆25Apr 26, 2023Updated 2 years ago
- Interface to OpenMM for easy setup of molecular dynamic simulations of protein-ligand complexes☆164Feb 1, 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
- An open-source platform for developing protein models beyond AlphaFold.☆12Jul 15, 2025Updated 7 months ago
- Genetic algorithm to convert 3D-RISM solvent densities to explicit water molecules in binding pockets☆12Dec 19, 2017Updated 8 years ago
- Notebooks demonstrating how to do simple tasks related to free energy calculations.☆64Feb 9, 2026Updated 2 weeks ago
- Plugin for folding sequences directly in PyMOL☆115Aug 4, 2025Updated 6 months ago
- Implementation of SCINS☆15Nov 6, 2024Updated last year
- Fold Conditioned protein design pipeline based on AF2Multimer Hallucination☆50Dec 2, 2025Updated 2 months ago
- ☆30Feb 6, 2026Updated 3 weeks ago
- Tool to predict water molecules placement and energy in ligand binding sites☆35Sep 16, 2025Updated 5 months ago
- Simulation-Enabled Estimation of Kinetic Rates - Version 2☆35Dec 10, 2025Updated 2 months ago
- ☆15Sep 26, 2025Updated 5 months ago
- Boltzmann-ranked alternative protein conformations from reduced-MSA AlphaFold2☆61Jan 30, 2026Updated last month
- ☆21Oct 9, 2025Updated 4 months ago
- Tools for coarse-grained molecular dynamics simulations using the SPICA force field☆13Apr 11, 2025Updated 10 months ago
- Structure prediction and design of proteins with noncanonical amino acids☆119Feb 1, 2026Updated last month
- The public versio☆82Jun 26, 2023Updated 2 years ago
- ☆15Jun 3, 2025Updated 8 months ago
- MAGPIE☆16May 5, 2024Updated last year
- POLYGON VAE For de novo Polypharmacology☆41Mar 5, 2025Updated 11 months ago
- Code for running BinderFlow☆62Nov 21, 2025Updated 3 months ago