Generative modeling of molecular dynamics trajectories
☆197Nov 23, 2025Updated 3 months ago
Alternatives and similar repositories for mdgen
Users that are interested in mdgen are comparing it to the libraries listed below
Sorting:
- AlphaFold Meets Flow Matching for Generating Protein Ensembles☆516Oct 21, 2025Updated 4 months ago
- This repository houses all the scripts and notebooks utilized for generating, analyzing, and validating the mdCATH dataset. Some user ex…☆57Dec 16, 2025Updated 2 months ago
- FoldFlow: SE(3)-Stochastic Flow Matching for Protein Backbone Generation☆274Dec 10, 2024Updated last year
- Benchmarking code accompanying the release of `bioemu`☆54Nov 25, 2025Updated 3 months ago
- ☆20Oct 3, 2024Updated last year
- [NeurIPS 2024] The implementation for the paper "Geometric Trajectory Diffusion Models".☆35Jul 22, 2025Updated 7 months ago
- Inference code for scalable emulation of protein equilibrium ensembles with generative deep learning☆753Updated this week
- Protein representation and design under a single training scheme☆24Updated this week
- AI-powered ab initio biomolecular dynamics simulation☆568Feb 18, 2025Updated last year
- Boltzmann-ranked alternative protein conformations from reduced-MSA AlphaFold2☆61Jan 30, 2026Updated last month
- Implementation for SE(3) diffusion model with application to protein backbone generation☆414Jul 3, 2023Updated 2 years ago
- Protein structure diffusion model for unconditional protein generation and motif scaffolding☆188Jun 24, 2024Updated last year
- Fast protein backbone generation with SE(3) flow matching.☆314Jul 19, 2024Updated last year
- ☆239Feb 12, 2026Updated 2 weeks ago
- NeurIPS 2023 Spotlight paper: Full atom protein pocket design via iterative refinement☆47Oct 28, 2023Updated 2 years ago
- Structure prediction of alternative protein conformations☆82Feb 24, 2025Updated last year
- Protein-ligand structure prediction☆238Jul 31, 2025Updated 7 months ago
- [ICML 25] We train and evaluate SAEs to identify interpretable features in pLMs and show their potential for scientific discovery.☆123Jan 16, 2026Updated last month
- Codebase of paper "Structure Language Models for Protein Conformation Generation" (ICLR'25)☆74Feb 24, 2025Updated last year
- All-atom protein generation using latent diffusion, with compositional function and taxonomic prompts. http://bit.ly/plaid-proteins☆120May 27, 2025Updated 9 months ago
- ☆27Oct 7, 2024Updated last year
- [ICML 2024] Floating Anchor Diffusion Model for Multi-motif Scaffolding☆31Aug 23, 2024Updated last year
- Deep generative modeling of protein structural ensembles☆36Sep 22, 2025Updated 5 months ago
- Diffusion-based all-atom protein generative model.☆232Aug 27, 2025Updated 6 months ago
- Sidechain conditioning and modeling for full-atom protein sequence design☆135Nov 11, 2025Updated 3 months ago
- NeuralPLexer: State-specific protein-ligand complex structure prediction with a multi-scale deep generative model☆324Oct 6, 2025Updated 4 months ago
- Diffusion model based protein-ligand flexible docking method☆116Oct 30, 2024Updated last year
- The official implementation of DiffAbXL benchmarked in the paper "Exploring Log-Likelihood Scores for Ranking Antibody Sequence Designs",…☆91Jun 11, 2025Updated 8 months ago
- Generate intrinsically disordered peptide conformations via machine learning☆24May 26, 2024Updated last year
- Implementation of DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain Packing☆89Dec 4, 2023Updated 2 years ago
- Efficient implementatin of ESM family.☆80Sep 9, 2025Updated 5 months ago
- A generative model for programmable protein design☆798Apr 11, 2024Updated last year
- Proteina is a new large-scale flow-based protein backbone generator that utilizes hierarchical fold class labels for conditioning and rel…☆236Jul 24, 2025Updated 7 months ago
- This repository provides with custom code and analysis scripts to generate structural ensembles of intrinsically disordered proteins by u…☆21Oct 31, 2025Updated 4 months ago
- Timewarp is a research project using deep learning to accelerate molecular dynamics simulation.☆59Aug 21, 2024Updated last year
- AlphaFold version that is extended to integrate diversity parameters for massive sampling.☆16Feb 13, 2026Updated 2 weeks ago
- ☆30Nov 23, 2025Updated 3 months ago
- Fast deep learning methods for large-scale protein-protein interaction screening☆118Aug 3, 2025Updated 7 months ago
- Learning the language of protein-protein interactions☆135Jan 12, 2026Updated last month