Code for Pre-training Protein Encoder via Siamese Sequence-Structure Diffusion Trajectory Prediction (https://arxiv.org/abs/2301.12068)
☆42Jul 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
Sorting:
- ☆18Feb 25, 2026Updated 3 weeks ago
- Graphormer Based Protein Sequence Design☆26Feb 2, 2024Updated 2 years ago
- Implementation of DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain Packing☆89Dec 4, 2023Updated 2 years ago
- Vabs-Net: Pre-Training Protein Bi-level Representation Through Span Mask Strategy On 3D Protein Chains☆18Sep 12, 2024Updated last year
- Source code of the paper "Protein Sequence and Structure Co-Design with Equivariant Translation"☆24Sep 18, 2023Updated 2 years ago
- A conditionally adapted protein language model for the generation of enzymes☆23Nov 26, 2024Updated last year
- Equivariant Scalar Fields for Molecular Docking with Fast Fourier Transforms☆31Dec 8, 2023Updated 2 years ago
- Generative diverse protein backbones by protein language model☆34Feb 27, 2026Updated 3 weeks 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☆415Jul 3, 2023Updated 2 years ago
- Fast protein backbone generation with SE(3) flow matching.☆317Jul 19, 2024Updated last year
- Codebase of the paper "Str2Str: A Score-based Framework for Zero-shot Protein Conformation Sampling" (ICLR 2024)☆81Mar 7, 2024Updated 2 years ago
- GearNet and Geometric Pretraining Methods for Protein Structure Representation Learning, ICLR'2023 (https://arxiv.org/abs/2203.06125)☆317Jun 13, 2025Updated 9 months ago
- Utility scripts to generate and evaluate parametrically guided beta barrel protein backbone structures.☆14Nov 14, 2025Updated 4 months ago
- A standardized protein design benchmark for motif-scaffolding problems☆76Jan 27, 2026Updated last month
- Pytorch implementation for ICML 2024 paper Proteus: Exploring Protein Structure Generation for Enhanced Designability and Efficiency.☆88Jun 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
- Sequence-Structure-Surface Model for Protein Fitness Prediction (S3F)☆47Dec 3, 2024Updated last year
- Implementation of methods to sample from Boltzmann distributions☆21Jan 24, 2023Updated 3 years ago
- [NeurIPS 2024] The implementation for the paper "Geometric Trajectory Diffusion Models".☆35Jul 22, 2025Updated 7 months 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☆117Mar 3, 2026Updated 2 weeks ago
- ☆244May 22, 2023Updated 2 years ago
- Toolkit for structure-based deep learning on RNA.☆45Feb 9, 2026Updated last month
- Deep generative modeling of protein structural ensembles☆37Sep 22, 2025Updated 5 months ago
- Geom3D: Geometric Modeling on 3D Structures, NeurIPS 2023☆131Jun 5, 2024Updated last year
- Joint Sequence-Structure Generation of Nucleic Acid and Protein Complexes with SE(3)-Discrete Diffusion☆60May 6, 2024Updated last year
- Protein structure datasets for machine learning.☆115Apr 22, 2025Updated 10 months ago
- ESM-GearNet for Protein Structure Representation Learning (https://arxiv.org/abs/2303.06275)☆111Oct 23, 2023Updated 2 years ago
- Protein representation and design under a single training scheme☆24Mar 3, 2026Updated 2 weeks ago
- ☆36Jun 17, 2025Updated 9 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 …☆267Apr 27, 2025Updated 10 months ago
- Implementation of Protein Invariant Point Packer (PIPPack)☆35May 28, 2024Updated last year
- 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☆72Mar 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…☆20Nov 24, 2025Updated 3 months ago