NuFold: End-to-End Approach for RNA Tertiary Structure Prediction with Flexible Nucleobase Center Representation
☆54Oct 31, 2025Updated 10 months ago
Alternatives and similar repositories for NuFold
Users that are interested in NuFold are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Nature Methods: RhoFold+, Accurate RNA 3D structure prediction using a language model-based deep learning approach☆245May 29, 2025Updated last year
- ARES implement in PyTorch☆17Feb 27, 2024Updated 2 years ago
- A Nextflow pipeline that creates reliable, structure-informed MSAs of thousands of protein sequences which can supplement structural info…☆11Jul 14, 2026Updated last month
- ☆15Jan 27, 2025Updated last year
- Official repo for paper "AlphaFold-Multimer accurately captures interactions and dynamics of intrinsically disordered protein regions"☆17Dec 8, 2024Updated last year
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- [ICML 2024] Floating Anchor Diffusion Model for Multi-motif Scaffolding☆34Aug 23, 2024Updated 2 years ago
- BioLiP2 database curation and web interface☆36Jun 19, 2025Updated last year
- ☆12May 3, 2025Updated last year
- protein backbone refinement☆16Sep 12, 2024Updated last year
- A protein structure dataset that combines 3D atomic coordinates with biophysical and evolutionary properties for every atom in every "cle…☆40Jul 25, 2024Updated 2 years ago
- Code associated with the publication 'Generative and predictive neural networks for the design of functional RNA molecules'☆15Apr 8, 2025Updated last year
- Kuhlman Lab Installation of AlphaFold3☆42Mar 26, 2026Updated 5 months ago
- A Light-Weight And Interpretable Molecular Docking Model☆26Oct 23, 2024Updated last year
- Weighted Ensemble Data Analysis and Plotting☆27Jul 17, 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.
- Neural Iterative Selection-Expansion using LigandMPNN/LASErMPNN and Boltz-2x☆68Aug 11, 2026Updated 3 weeks ago
- ☆13May 18, 2025Updated last year
- Computational Chemistry Workflows☆57Jul 19, 2022Updated 4 years ago
- Scaffold decoration and fragment linking with chemical language models and RL☆28Mar 24, 2025Updated last year
- Nextflow pipeline for the computation of structure-based MSAs with AlphaFold2 models☆13Dec 20, 2022Updated 3 years ago
- Design a local part of a protein☆20Jan 12, 2023Updated 3 years ago
- Explore protein fold space with deep generative models☆16Aug 5, 2024Updated 2 years ago
- Display PackedPose objects, Pose objects, or PDB files within a Jupyter notebook and Google Colab☆11Aug 29, 2026Updated last week
- Interface-aware molecular generative framework for protein-protein interaction modulators☆20Dec 22, 2024Updated last year
- 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.
- PDBench is a dataset and software package for evaluating fixed-backbone sequence design algorithms.☆33Jan 17, 2023Updated 3 years ago
- mdml: Deep Learning for Molecular Simulations☆55May 17, 2025Updated last year
- AnnapuRNA: a scoring function for predicting RNA-small molecule interactions.☆21Apr 5, 2024Updated 2 years ago
- ☆53Jun 17, 2026Updated 2 months ago
- Official code repository for the paper Molecule Generation with Fragment Retrieval Augmentation (NeurIPS 2024)☆31Apr 2, 2025Updated last year
- A Python program for QM/MM Simulations based on the Perturbed Matrix Method☆27Oct 17, 2023Updated 2 years ago
- A snakemake-based workflow for FEP and MM(PB/GB)SA calculations with GROMACS☆169May 9, 2026Updated 3 months ago
- Code release for "Improving diffusion-based protein backbone generation with global-geometry-aware latent encoding"☆48Aug 5, 2025Updated last year
- UCBShift is a program for predicting chemical shifts for backbone atoms and β-carbon of a protein in solution. It utilizes a machine lear…☆28Aug 13, 2026Updated 3 weeks ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Geometric Algebra Flow Matching (GAFL) for Protein Backbone Generation☆20May 5, 2026Updated 4 months ago
- A comprehensive Model Context Protocol (MCP) server providing advanced access to the UniProt protein database.☆20Dec 21, 2025Updated 8 months ago
- Basic RNA 3D structure comparison metrics in RNA-Puzzles, including INF, DI and RMSD. It also includes `RNA_normalizer` tool in pdb_utils…☆27Dec 3, 2024Updated last year
- Molecular Dynamics for Experimentalists☆72Jul 28, 2026Updated last month
- DSDPFlex: Flexible-Receptor Docking with GPU Acceleration☆26Dec 24, 2025Updated 8 months ago
- ☆15Apr 17, 2025Updated last year
- Python package wrapping the DOCK Fortran program and providing several tools built on top of it.☆17Jan 16, 2026Updated 7 months ago