A command-line interface and Python library for generating AlphaFold3 input files.
☆41Jan 2, 2026Updated 6 months ago
Alternatives and similar repositories for af3cli
Users that are interested in af3cli are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Complete saturation mutagenesis of a protein using ESM☆18Feb 20, 2024Updated 2 years ago
- Official repository of GENzyme☆65Nov 29, 2024Updated last year
- Utility scripts to generate and evaluate parametrically guided beta barrel protein backbone structures.☆13Nov 14, 2025Updated 8 months ago
- 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
- Shrinking Proteins with Diffusion☆29Jan 8, 2026Updated 6 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.
- Diffusion model based protein-ligand flexible docking method☆118Oct 30, 2024Updated last year
- Scoring function for interprotein interactions in AlphaFold2 and AlphaFold3☆251Jan 3, 2026Updated 6 months ago
- Official repo for paper "AlphaFold-Multimer accurately captures interactions and dynamics of intrinsically disordered protein regions"☆17Dec 8, 2024Updated last year
- de novo design of high affinity biological binders☆187Jun 22, 2026Updated 3 weeks ago
- Code for running PottsMPNN to generate sequences and predict energies☆23Jun 20, 2026Updated last month
- Deep generative modeling of protein structural ensembles☆39May 27, 2026Updated last month
- Prediction of protein melting temperatures directly from sequences☆14Apr 16, 2024Updated 2 years ago
- ☆151Jul 16, 2025Updated last year
- ☆136Jun 9, 2026Updated last month
- 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.
- A Score-Only Adaptation of AlphaFold3 for Biomolecular Structure Evaluation☆129Jan 28, 2026Updated 5 months ago
- code and source data for de novo design of Kemp elimination paper☆26Sep 18, 2025Updated 10 months ago
- ☆28Mar 21, 2025Updated last year
- Energy-guided binder design pipeline built on BindCraft☆18Jun 6, 2025Updated last year
- Multimodal Pretraining for Unsupervised Protein Representation Learning☆22Jul 30, 2024Updated last year
- Toolkit for alphafold3 input and output files☆105Updated this week
- Predict multiple protein conformations using sequence clustering and AlphaFold2.☆189Oct 7, 2025Updated 9 months ago
- [ICML 2024] Floating Anchor Diffusion Model for Multi-motif Scaffolding☆34Aug 23, 2024Updated last year
- Sequence-Structure-Surface Model for Protein Fitness Prediction (S3F)☆53Dec 3, 2024Updated last year
- 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.
- Public RFDiffusionAA repo☆483Jul 9, 2024Updated 2 years ago
- Template-based protein design with Raygun☆84Apr 12, 2026Updated 3 months ago
- ☆33Mar 2, 2026Updated 4 months ago
- A conditionally adapted protein language model for the generation of enzymes☆24Nov 26, 2024Updated last year
- A tool for 2D protein visualization aimed at improving the comparability of protein structures through standardized 2D visualizations.☆22Mar 13, 2026Updated 4 months ago
- Diffusion-based all-atom protein generative model.☆236Aug 27, 2025Updated 10 months ago
- ☆605Feb 6, 2025Updated last year
- EnzyHTP is a python library that automates the complete life-cycle of enzyme modeling☆36Jul 2, 2026Updated 2 weeks ago
- pdbx is a parser module in python for structures of the protein data bank in the mmcif format☆31Aug 9, 2024Updated last year
- 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.
- Pytorch implementation for ICML 2024 paper Proteus: Exploring Protein Structure Generation for Enhanced Designability and Efficiency.☆90Jun 23, 2024Updated 2 years ago
- A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD☆16Apr 3, 2026Updated 3 months ago
- AlphaFold-initiated replica exchange protein docking☆92Jun 5, 2025Updated last year
- ☆98Oct 14, 2025Updated 9 months ago
- DDGScan: an integrated parallel workflow for the in silico point mutation scan of protein☆50Mar 21, 2024Updated 2 years ago
- The official implementation of DiffAbXL benchmarked in the paper "Exploring Log-Likelihood Scores for Ranking Antibody Sequence Designs",…☆100Jun 11, 2025Updated last year
- Boltzmann-ranked alternative protein conformations from reduced-MSA AlphaFold2☆63Apr 6, 2026Updated 3 months ago