From bf384f761c69a97778d68e356833d5d421ca13b6 Mon Sep 17 00:00:00 2001 From: cmunley1 Date: Sun, 11 Jan 2026 13:30:01 -0800 Subject: [PATCH 1/4] Update README.md --- README.md | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 4fbe470..f0dd8cf 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ ### Model Description RNAPro is a state-of-the-art RNA 3D folding model developed in collaboration with the hosts and winners of the [Stanford RNA 3D Folding Kaggle competition. -](https://www.kaggle.com/competitions/stanford-rna-3d-folding) The model incorporates RNA-specific modules — including template modeling, multiple sequence alignment (MSA), and a pretrained RNA language model — to enhance RNA structure prediction performance. Read more about the kaggle competition and model in the [preprint](https://www.biorxiv.org/content/10.64898/2025.12.30.696949v1). +](https://www.kaggle.com/competitions/stanford-rna-3d-folding) RNAPro uses a frozen pre-trained RNA foundation model RibonanzaNet2 as an encoder to extract RNA sequence and pairwise features. These are projected and injected into a RNA post-trained Protenix with learned gating. A configurable RNA template encoder and MSA pipeline are used to enhance the structure prediction accuracy. Read more about the kaggle competition and model in the [preprint](https://www.biorxiv.org/content/10.64898/2025.12.30.696949v1). ## Installation @@ -38,7 +38,6 @@ Run step 1., and inside the container, run step 3. For more detailed instruction steps, check the [Docker Installation](docs/docker_installation.md) guide. - ## Train Models ### 1. Data preparation @@ -250,4 +249,4 @@ We thank Stanford Das Lab, HHMI, the co-hosts and winners of the Stanford RNA 3D Copyright (c) 2026 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
The source code is made available under Apache-2.0.
-The model weights are made available under the [NVIDIA Open Model License](https://www.nvidia.com/en-us/agreements/enterprise-software/nvidia-open-model-license/). \ No newline at end of file +The model weights are made available under the [NVIDIA Open Model License](https://www.nvidia.com/en-us/agreements/enterprise-software/nvidia-open-model-license/). From 72c3aee699aa6b20a506bd5e53ae79b101039ac2 Mon Sep 17 00:00:00 2001 From: cmunley1 Date: Sun, 11 Jan 2026 13:30:23 -0800 Subject: [PATCH 2/4] Update README.md --- README.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/README.md b/README.md index f0dd8cf..4170051 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,7 @@ # RNAPro: An accurate RNA structure prediction model by Kaggle synthesis ### Model Description -RNAPro is a state-of-the-art RNA 3D folding model developed in collaboration with the hosts and winners of the [Stanford RNA 3D Folding Kaggle competition. -](https://www.kaggle.com/competitions/stanford-rna-3d-folding) RNAPro uses a frozen pre-trained RNA foundation model RibonanzaNet2 as an encoder to extract RNA sequence and pairwise features. These are projected and injected into a RNA post-trained Protenix with learned gating. A configurable RNA template encoder and MSA pipeline are used to enhance the structure prediction accuracy. Read more about the kaggle competition and model in the [preprint](https://www.biorxiv.org/content/10.64898/2025.12.30.696949v1). +RNAPro is a state-of-the-art RNA 3D folding model developed in collaboration with the hosts and winners of the [Stanford RNA 3D Folding Kaggle competition.](https://www.kaggle.com/competitions/stanford-rna-3d-folding) RNAPro uses a frozen pre-trained RNA foundation model RibonanzaNet2 as an encoder to extract RNA sequence and pairwise features. These are projected and injected into a RNA post-trained Protenix with learned gating. A configurable RNA template encoder and MSA pipeline are used to enhance the structure prediction accuracy. Read more about the kaggle competition and model in the [preprint](https://www.biorxiv.org/content/10.64898/2025.12.30.696949v1). ## Installation From 1cf2b413bce277eca1810eadcc6a9126ed65c5ea Mon Sep 17 00:00:00 2001 From: Youhan Lee Date: Wed, 14 Jan 2026 16:47:43 +0900 Subject: [PATCH 3/4] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 4170051..37458a3 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ # RNAPro: An accurate RNA structure prediction model by Kaggle synthesis ### Model Description -RNAPro is a state-of-the-art RNA 3D folding model developed in collaboration with the hosts and winners of the [Stanford RNA 3D Folding Kaggle competition.](https://www.kaggle.com/competitions/stanford-rna-3d-folding) RNAPro uses a frozen pre-trained RNA foundation model RibonanzaNet2 as an encoder to extract RNA sequence and pairwise features. These are projected and injected into a RNA post-trained Protenix with learned gating. A configurable RNA template encoder and MSA pipeline are used to enhance the structure prediction accuracy. Read more about the kaggle competition and model in the [preprint](https://www.biorxiv.org/content/10.64898/2025.12.30.696949v1). +RNAPro is a state-of-the-art RNA 3D folding model developed in collaboration with the hosts and winners of the [Stanford RNA 3D Folding Kaggle competition.](https://www.kaggle.com/competitions/stanford-rna-3d-folding) RNAPro combines RNA-specific modules — including template modeling, multiple sequence alignment (MSA), and a pretrained RNA foundation model, especially, RibonanzaNet2 — with Protenix to enhance RNA structure prediction performance. Read more about the kaggle competition and model in the [preprint](https://www.biorxiv.org/content/10.64898/2025.12.30.696949v1). ## Installation From 8c6db867b41c371e8e5e5d4a8a2c9e9993abbd14 Mon Sep 17 00:00:00 2001 From: Youhan Lee Date: Wed, 14 Jan 2026 16:52:13 +0900 Subject: [PATCH 4/4] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 37458a3..4e81352 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ # RNAPro: An accurate RNA structure prediction model by Kaggle synthesis ### Model Description -RNAPro is a state-of-the-art RNA 3D folding model developed in collaboration with the hosts and winners of the [Stanford RNA 3D Folding Kaggle competition.](https://www.kaggle.com/competitions/stanford-rna-3d-folding) RNAPro combines RNA-specific modules — including template modeling, multiple sequence alignment (MSA), and a pretrained RNA foundation model, especially, RibonanzaNet2 — with Protenix to enhance RNA structure prediction performance. Read more about the kaggle competition and model in the [preprint](https://www.biorxiv.org/content/10.64898/2025.12.30.696949v1). +RNAPro is a state-of-the-art RNA 3D folding model developed in collaboration with the hosts and winners of the [Stanford RNA 3D Folding Kaggle competition.](https://www.kaggle.com/competitions/stanford-rna-3d-folding) RNAPro combines RNA-specific modules including template modeling, multiple sequence alignment (MSA), and a pretrained RNA foundation model, especially, RibonanzaNet2 with Protenix to enhance RNA structure prediction performance. Read more about the kaggle competition and model in the [preprint](https://www.biorxiv.org/content/10.64898/2025.12.30.696949v1). ## Installation