Code for Pre-training Protein Encoder via Siamese Sequence-Structure Diffusion Trajectory Prediction (https://arxiv.org/abs/2301.12068)
☆41Jul 9, 2023Updated 2 years ago
Alternatives and similar repositories for SiamDiff
Users that are interested in SiamDiff are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Graphormer Based Protein Sequence Design☆26Feb 2, 2024Updated 2 years ago
- Implementation of DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain Packing☆90Dec 4, 2023Updated 2 years ago
- 🧬 Large-scale protein functional residue or fragment prediction benchmark. (ICLR 2026)☆24Apr 10, 2026Updated last month
- Vabs-Net: Pre-Training Protein Bi-level Representation Through Span Mask Strategy On 3D Protein Chains☆17Sep 12, 2024Updated last year
- Source code of the paper "Protein Sequence and Structure Co-Design with Equivariant Translation"☆24Sep 18, 2023Updated 2 years ago
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- A conditionally adapted protein language model for the generation of enzymes☆24Nov 26, 2024Updated last year
- Equivariant Scalar Fields for Molecular Docking with Fast Fourier Transforms☆31Dec 8, 2023Updated 2 years ago
- Sequence-Structure-Surface Model for Protein Fitness Prediction (S3F)☆52Dec 3, 2024Updated last year
- Generative diverse protein backbones by protein language model☆35Feb 27, 2026Updated 3 months ago
- Generative Pretrained Autoregressive Transformer Graph Neural Network applied to the Analysis and Discovery of Materials☆16Aug 9, 2023Updated 2 years ago
- Intrinsic-Extrinsic Convolution and Pooling for Learning on 3D Protein Structures☆49Jan 24, 2022Updated 4 years ago
- Aligned Diffusion Schroedinger Bridges (UAI 2023)☆33Oct 1, 2023Updated 2 years ago
- Implementation for SE(3) diffusion model with application to protein backbone generation☆421Jul 3, 2023Updated 2 years ago
- Fast protein backbone generation with SE(3) flow matching.☆326Jul 19, 2024Updated last year
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Codebase of the paper "Str2Str: A Score-based Framework for Zero-shot Protein Conformation Sampling" (ICLR 2024)☆85Apr 21, 2026Updated last month
- Utility scripts to generate and evaluate parametrically guided beta barrel protein backbone structures.☆13Nov 14, 2025Updated 6 months ago
- GearNet and Geometric Pretraining Methods for Protein Structure Representation Learning, ICLR'2023 (https://arxiv.org/abs/2203.06125)☆319Jun 13, 2025Updated 11 months ago
- A standardized protein design benchmark for motif-scaffolding problems☆79Updated this week
- Pytorch implementation for ICML 2024 paper Proteus: Exploring Protein Structure Generation for Enhanced Designability and Efficiency.☆90Jun 23, 2024Updated last year
- Code implementation of "Diffusion probabilistic modeling of protein backbones in 3D for the motif-scaffolding problem" https://arxiv.org/…☆74Aug 11, 2023Updated 2 years ago
- Implementation of methods to sample from Boltzmann distributions☆22Jan 24, 2023Updated 3 years ago
- ☆11Aug 3, 2023Updated 2 years ago
- A collection of tasks to probe the effectiveness of protein sequence representations in modeling aspects of protein design☆125Apr 23, 2026Updated last month
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- [NeurIPS 2024] The implementation for the paper "Geometric Trajectory Diffusion Models".☆38Jul 22, 2025Updated 10 months ago
- Toolkit for structure-based deep learning on RNA.☆47May 13, 2026Updated 3 weeks ago
- ☆248May 22, 2023Updated 3 years ago
- Deep generative modeling of protein structural ensembles☆37May 27, 2026Updated last week
- Geom3D: Geometric Modeling on 3D Structures, NeurIPS 2023☆130Jun 5, 2024Updated 2 years ago
- Joint Sequence-Structure Generation of Nucleic Acid and Protein Complexes with SE(3)-Discrete Diffusion☆60May 6, 2024Updated 2 years ago
- Protein structure datasets for machine learning.☆114Apr 22, 2025Updated last year
- ESM-GearNet for Protein Structure Representation Learning (https://arxiv.org/abs/2303.06275)☆114Oct 23, 2023Updated 2 years ago
- Protein representation and design under a single training scheme☆24May 17, 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.
- ☆40Jun 17, 2025Updated 11 months ago
- This repo contains the collection of codes to find designer interfacial mutations☆17Sep 4, 2023Updated 2 years ago
- Benchmarking framework for protein representation learning. Includes a large number of pre-training and downstream task datasets, models …☆273Apr 27, 2025Updated last year
- Implementation of Protein Invariant Point Packer (PIPPack)☆35May 28, 2024Updated 2 years ago
- Repository for Protein-Vec, a protein embedding mixture of experts model☆38Jan 24, 2024Updated 2 years ago
- Pretrainable geometric graph neural network for antibody affinity maturation☆77Mar 18, 2025Updated last year
- BC-Design: A Biochemistry-Aware Framework for High-Precision Inverse Protein Folding https://www.biorxiv.org/content/10.1101/2024.10.28.6…☆21Nov 24, 2025Updated 6 months ago