Python code to run Thermal Titration Molecular Dynamics (TTMD) simulations
☆20Feb 25, 2026Updated 3 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:
- Neural Iterative Selection-Expansion using LigandMPNN/LASErMPNN and Boltz-2x☆33May 11, 2026Updated 3 weeks ago
- Input files and binding free energy values from our benchmark with QuantumBind-RBFE☆16Apr 16, 2025Updated last year
- P2DFlow: A Protein Ensemble Generative Model with SE(3) Flow Matching☆44May 22, 2025Updated last year
- A geometric flow matching model for generative protein-ligand docking and affinity prediction. (ISMB 2025)☆137Sep 3, 2025Updated 9 months ago
- Protein design and sculpting using Rosetta and Deep learning methods (RFDiff and Alphafold2)☆55Jun 1, 2026Updated last week
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- Code for the paper "Learning to engineer protein flexibility".☆22Mar 24, 2026Updated 2 months ago
- All-Atom (Including Hydrogen!) Ligand-Conditioned Protein Sequence Design & Sidechain Packing GNN☆29Updated this week
- ParametrizANI - Fast, Accurate and Free Dihedral Parametrization in the Cloud with TorchANI☆22Jul 28, 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
- Interface to OpenMM for easy setup of molecular dynamic simulations of protein-ligand complexes☆172May 22, 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
- Physics-Guided All-Atom Diffusion Model for Accurate Protein-Ligand Complex Prediction☆90Oct 6, 2025Updated 8 months 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☆121May 1, 2026Updated last month
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- Notebooks demonstrating how to do simple tasks related to free energy calculations.☆68Updated this week
- ☆50Nov 19, 2025Updated 6 months ago
- A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD☆16Apr 3, 2026Updated 2 months ago
- ESMDynamic repo☆23Apr 28, 2026Updated last month
- ☆26Apr 26, 2023Updated 3 years ago
- ReaSyn is a model for predicting a molecule's synthesis pathway, reaction steps from building blocks to final product(s), using an encode…☆98Jan 11, 2026Updated 4 months ago
- An open-source platform for developing protein models beyond AlphaFold.☆12Jul 15, 2025Updated 10 months ago
- Implementation of SCINS☆16Nov 6, 2024Updated last year
- Tool to predict water molecules placement and energy in ligand binding sites☆36Sep 16, 2025Updated 8 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.
- SableBind is an open-source framework dedicated to predicting protein-ligand binding affinity☆13Feb 6, 2025Updated last year
- ☆16Sep 26, 2025Updated 8 months ago
- AbBFN2: A flexible antibody foundation model based on Bayesian Flow Networks☆40Jun 4, 2025Updated last year
- Plugin for folding sequences directly in PyMOL☆118Aug 4, 2025Updated 10 months ago
- Simulation-Enabled Estimation of Kinetic Rates - Version 2☆35Dec 10, 2025Updated 6 months ago
- Tools for coarse-grained molecular dynamics simulations using the SPICA force field☆13May 12, 2026Updated 3 weeks ago
- ☆14May 18, 2026Updated 3 weeks ago
- Fold Conditioned protein design pipeline based on AF2Multimer Hallucination☆53Mar 25, 2026Updated 2 months ago
- ☆15Jun 3, 2025Updated last year
- 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.
- Code for running BinderFlow☆66Nov 21, 2025Updated 6 months ago
- Repo for the publication titled: "Key Interaction Networks: Identifying Evolutionarily Conserved Non-Covalent Interaction Networks Across…☆18Nov 14, 2023Updated 2 years ago
- ☆32May 25, 2026Updated 2 weeks ago
- Density based object completion over PBC.☆31Apr 23, 2026Updated last month
- ☆29Jul 28, 2023Updated 2 years ago
- ☆68Apr 28, 2025Updated last year
- MAGPIE☆17May 5, 2024Updated 2 years ago