Exploring the Alignment of Generation and Understanding in Protein Structure Modeling | Paper Citation Record

Observation 466d8429-58c7-4c9f-bef3-f13dee455774 · outbound

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Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Gene ontology: tool for the unification of biology.Nature genetics, 25(1):25–29, 2000

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Observation ab59846e-64be-40a0-95c7-0df8617bd54c · outbound

This paper cites Self-supervised learning from images with a joint- embedding predictive architecture.

Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Self-supervised learning from images with a joint- embedding predictive architecture

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Exploring the Alignment of Generation and Understanding in Protein Structure Modeling The enzyme database in 2000.Nucleic acids research, 28(1):304–305, 2000

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This paper cites All are worth words: A vit backbone for diffusion models.

Exploring the Alignment of Generation and Understanding in Protein Structure Modeling All are worth words: A vit backbone for diffusion models

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Observation 34dc8e58-28a3-4160-b6be-625cd6ffe1c4 · outbound

This paper cites SE(3)-Stochastic Flow Matching for Protein Backbone Generation.

Exploring the Alignment of Generation and Understanding in Protein Structure Modeling SE(3)-Stochastic Flow Matching for Protein Backbone Generation

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Observation 127abfb3-86cc-499b-9d58-17f2fdc4d9e0 · outbound

This paper cites Deconstructing Denoising Diffusion Models for Self-Supervised Learning.

Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Deconstructing Denoising Diffusion Models for Self-Supervised Learning

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This paper cites Robust deep learning–based protein sequence design using proteinmpnn.Science, 378(6615):49–56, 2022.

Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Robust deep learning–based protein sequence design using proteinmpnn.Science, 378(6615):49–56, 2022

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Observation e567b871-e26f-475c-9109-c3aa840a8781 · outbound

This paper cites Flow autoencoders are effective protein tokenizers.arXiv preprint arXiv:2510.00351, 2025.

Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Flow autoencoders are effective protein tokenizers.arXiv preprint arXiv:2510.00351, 2025

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This paper cites Atomica: Learning universal representations of intermolecular interactions.bioRxiv, pages 2025–04, 2025.

Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Atomica: Learning universal representations of intermolecular interactions.bioRxiv, pages 2025–04, 2025

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Observation d6a7a5d4-14b5-4ac8-9677-c1369d7d21c4 · outbound

This paper cites Foldtoken: Learning protein language via vector quantization and beyond.

Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Foldtoken: Learning protein language via vector quantization and beyond

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Observation c72e129b-a1df-4259-bbcb-acdd1bb13a3d · outbound

This paper cites Learning the Language of Protein Structure.

Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Learning the Language of Protein Structure

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Observation d7be091a-bf04-41f1-836b-f31f953a7413 · outbound

This paper cites La-Proteina: Atomistic Protein Generation via Partially Latent Flow Matching.

Exploring the Alignment of Generation and Understanding in Protein Structure Modeling La-Proteina: Atomistic Protein Generation via Partially Latent Flow Matching

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Observation 2b6890e9-33a1-42a1-a81a-7cfcc02c8cab · outbound

This paper cites Simulating 500 million years of evolution with a language model.Science, 387(6736):850–858, 2025.

Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Simulating 500 million years of evolution with a language model.Science, 387(6736):850–858, 2025

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Observation f0ca586d-0883-4b3e-a742-45219a05dd62 · outbound

This paper cites Bilingual language model for protein sequence and structure.NAR Genomics and Bioinformatics, 6(4):lqae150, 2024.

Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Bilingual language model for protein sequence and structure.NAR Genomics and Bioinformatics, 6(4):lqae150, 2024

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Observation 8dfe2d4d-6766-4f27-b7e1-86ad7e6fa487 · outbound

This paper cites Contrastive Representation Learning for 3D Protein Structures.

Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Contrastive Representation Learning for 3D Protein Structures

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This paper cites The coming of age of de novo protein design.

Exploring the Alignment of Generation and Understanding in Protein Structure Modeling The coming of age of de novo protein design

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This paper cites Sequence-augmented se (3)-flow matching for conditional protein generation.Advances in neural information processing systems, 37:33007–33036, 2024.

Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Sequence-augmented se (3)-flow matching for conditional protein generation.Advances in neural information processing systems, 37:33007–33036, 2024

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This paper cites Illumi- nating protein space with a programmable generative model.Nature, 623(7989):1070–1078, 2023.

Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Illumi- nating protein space with a programmable generative model.Nature, 623(7989):1070–1078, 2023

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This paper cites Evaluating representation learning on the protein structure universe.ArXiv, pages arXiv–2406, 2024.

Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Evaluating representation learning on the protein structure universe.ArXiv, pages arXiv–2406, 2024

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Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Highly accurate protein structure prediction with alphafold.nature, 596(7873):583–589, 2021

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Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Elucidating the design space of diffusion-based generative models.Advances in neural information processing systems, 35:26565–26577, 2022

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Observation 07dd5fa4-c4ed-412d-91f0-b7a2724133e7 · outbound

This paper cites Adam: A Method for Stochastic Optimization.

Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Adam: A Method for Stochastic Optimization

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Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Repa-e: Unlocking vae for end-to-end tuning of latent diffusion transformers

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Observation 948b7896-22b1-4baf-a2c6-fc35f675e780 · outbound

This paper cites Your diffusion model is secretly a zero-shot classifier.

Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Your diffusion model is secretly a zero-shot classifier

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Observation e7db3650-8a75-4b03-ae0d-ae885cb915b7 · outbound

This paper cites Out of Many, One: Designing and Scaffolding Proteins at the Scale of the Structural Universe with Genie 2.

Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Out of Many, One: Designing and Scaffolding Proteins at the Scale of the Structural Universe with Genie 2

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Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Evolutionary-scale prediction of atomic-level protein structure with a language model.Science, 379(6637):1123–1130, 2023

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Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Structure Language Models for Protein Conformation Generation

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Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Assessing generative model coverage of protein structures with shapes.Cell Systems, 16(8), 2025

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Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Conditional protein structure generation with protpardelle-1c.bioRxiv, 2025

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Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Bioto- ken and biofm–biologically-informed tokenization enables accurate and efficient genomic foundation models.bioRxiv, pages 2025–03, 2025

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Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Machine learning for functional protein design.Nature biotechnology, 42(2):216–228, 2024

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Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Gcc: Graph contrastive coding for graph neural network pre-training

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Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Instructplm: Aligning protein language models to follow protein structure instructions.bioRxiv, pages 2024–04, 2024

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Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Deep learning enables high-quality and high-throughput prediction of enzyme commission numbers.Proceedings of the National Academy of Sciences, 116(28):13996–14001, 2019

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Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Fine-tuning protein language models boosts predictions across diverse tasks.Nature Communications, 15(1):7407, 2024

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Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Cath: increased structural coverage of functional space.Nucleic acids research, 49(D1):D266–D273, 2021

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Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Saprot: Protein language modeling with structure-aware vocabulary.BioRxiv, pages 2023–10, 2023

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Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Scaling text-to-image diffusion transformers with representation autoencoders.arXiv preprint arXiv:2601.16208, 2026

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Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Neural discrete representation learning.Advances in neural information processing systems, 30, 2017

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Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Foldseek: fast and accurate protein structure search.Biorxiv, pages 2022–02, 2022

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Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Fast and accurate protein structure search with foldseek.Nature biotechnology, 42(2):243–246, 2024

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Exploring the Alignment of Generation and Understanding in Protein Structure Modeling DPLM-2: A Multimodal Diffusion Protein Language Model

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Exploring the Alignment of Generation and Understanding in Protein Structure Modeling De novo design of protein structure and function with rfdiffusion.Nature, 620(7976):1089–1100, 2023

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Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Sidechain conditioning and modeling for full-atom protein sequence design with fampnn.Proceedings of machine learning research, 267:66746, 2025

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Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Generative artificial intelligence for de novo protein design.Current Opinion in Structural Biology, 86:102794, 2024

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Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Denoising diffusion autoencoders are unified self-supervised learners

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Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Fast protein backbone generation with SE(3) flow matching

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Exploring the Alignment of Generation and Understanding in Protein Structure Modeling SE(3) diffusion model with application to protein backbone generation

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Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Graph contrastive learning with augmentations.Advances in neural information processing systems, 33:5812–5823, 2020

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Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Representation Alignment for Generation: Training Diffusion Transformers Is Easier Than You Think

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Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Enzyme function prediction using contrastive learning.Science, 379(6639):1358–1363, 2023

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Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Protein Representation Learning by Geometric Structure Pretraining

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Exploring the Alignment of Generation and Understanding in Protein Structure Modeling Diffusion Transformers with Representation Autoencoders

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Exploring the Alignment of Generation and Understanding in Protein Structure Modeling MotifBench: A standardized protein design benchmark for motif-scaffolding problems

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