docs: add O2' post-processing guide and update contributing/acknowled…

CONTRIBUTING.md

@@ -1,13 +1,82 @@
-# Contributing
+# Contribution Rules
 
-This repository is currently published as a read-only project. We do not accept external code or documentation contributions at this time.
+## Issue Tracking
 
-## Do
-- Do open an Issue for reproducible bugs using the Bug Report template.
-- Do include environment details, steps to reproduce, and minimal examples.
-- Do cite this work in academic use.
+* All requests for enhancements, bug fixes, or features must begin with the creation of an [issue](https://github.com/NVIDIA-BioNeMo/RNAPro/issues).
+  * The issue request will be reviewed by the NVIDIA team and approved prior to pull request integration and code review.
 
-## Don't
-- Don’t open Pull Requests — they will be auto-closed.
-- Don’t file feature requests or support requests outside the Issue template scope.
-- Don’t share proprietary data or confidential information in Issues.
+
+## Coding Guidelines
+
+- Avoid introducing unnecessary complexity into existing code so that maintainability and readability are preserved.
+
+- Try to keep pull requests (PRs) as concise as possible:
+  - Avoid committing commented-out code.
+  - Wherever possible, each PR should address a single concern. If there are several otherwise-unrelated things that should be fixed to reach a desired endpoint, our recommendation is to open several PRs and indicate the dependencies in the description. The more complex the changes are in a single PR, the more time it will take to review those changes.
+
+- Make sure that you can contribute your work to open source (no license and/or patent conflict is introduced by your code). You will need to [`sign`](#signing-your-work) your commit.
+
+- Thanks in advance for your patience as we review your contributions; we do appreciate them!
+
+
+## Pull Requests
+Developer workflow for code contributions is as follows:
+
+1. Developers must first [fork](https://help.github.com/en/articles/fork-a-repo) the [upstream](https://github.com/NVIDIA-BioNeMo/RNAPro) RNAPro repository.
+
+2. Git clone the forked repository and push changes to the personal fork.
+
+```bash
+git clone https://github.com/YOUR_USERNAME/YOUR_FORK.git RNAPro
+# Checkout the targeted branch and commit changes
+# Push the commits to a branch on the fork (remote).
+git push -u origin <local-branch>:<remote-branch>
+```
+
+3. Once the code changes are staged on the fork and ready for review, a [Pull Request](https://help.github.com/en/articles/about-pull-requests) (PR) can be [requested](https://help.github.com/en/articles/creating-a-pull-request) to merge the changes from a branch of the fork into a selected branch of upstream.
+  * Exercise caution when selecting the source and target branches for the PR.
+  * Creation of a PR creation kicks off the code review process.
+  * While under review, mark your PRs as work-in-progress by prefixing the PR title with [WIP].
+
+
+## Signing Your Work
+We require that all contributors "sign-off" on their commits. This certifies that the contribution is your original work, or you have rights to submit it under the same license, or a compatible license.
+Any contribution which contains commits that are not Signed-Off will not be accepted.
+
+To sign off on a commit you simply use the `--signoff` (or `-s`) option when committing your changes:
+```bash
+$ git commit -s -m "Add cool feature."
+```
+
+This will append the following to your commit message:
+```
+Signed-off-by: Your Name <your@email.com>
+```
+
+#### Full text of the DCO
+
+```
+Developer Certificate of Origin
+Version 1.1
+
+Copyright (C) 2004, 2006 The Linux Foundation and its contributors.
+1 Letterman Drive
+Suite D4700
+San Francisco, CA, 94129
+
+Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.
+```
+
+```
+Developer's Certificate of Origin 1.1
+
+By making a contribution to this project, I certify that:
+
+(a) The contribution was created in whole or in part by me and I have the right to submit it under the open source license indicated in the file; or
+
+(b) The contribution is based upon previous work that, to the best of my knowledge, is covered under an appropriate open source license and I have the right under that license to submit that work with modifications, whether created in whole or in part by me, under the same open source license (unless I am permitted to submit under a different license), as indicated in the file; or
+
+(c) The contribution was provided directly to me by some other person who certified (a), (b) or (c) and I have not modified it.
+
+(d) I understand and agree that this project and the contribution are public and that a record of the contribution (including all personal information I submit with it, including my sign-off) is maintained indefinitely and may be redistributed consistent with this project or the open source license(s) involved.
+```

README.md

@@ -245,10 +245,39 @@ RNAPro uses a frozen pre-trained RNA foundation model RibonanzaNet2 as an encode
 ```
 
 
+
 ## Acknowledgements
 
 We thank Stanford Das Lab, HHMI, the co-hosts and winners of the Stanford RNA 3D Folding Kaggle competition for their collaboration in this research.
 
+For the full list of authors and contributors to the research, please refer to the preprint.
+
+### Code Contributors
+
+We specifically thank the following people for direct code contributions to RNAPro:
+
+- **NVIDIA:** Youhan Lee, Christian Munley, Theo Viel, Emine Küçükbenli
+- **Das Lab (Stanford):** Rhiju Das, Chaitanya K. Joshi (Cambridge during development; now Stanford Das Lab)
+
+
+## Citation
+
+If you use RNAPro, please cite the preprint:
+
+```bibtex
+@article{Lee2025.12.30.696949,
+  author = {Lee, Youhan and He, Shujun and Oda, Toshiyuki and Rao, G. John and Kim, Yehyun and Kim, Raehyun and Kim, Hyunjin and Heng, Cher Keng and Kowerko, Danny and Li, Haowei and Nguyen, Hoa and Sampathkumar, Arunodhayan and Enrique G{\'o}mez, Ra{\'u}l and Chen, Meng and Yoshizawa, Atsushi and Kuraishi, Shun and Ogawa, Kenji and Zou, Shuxian and Paullier, Alejo and Zhao, Bingkang and Chen, Huey-Long and Hsu, Tsu-An and Hirano, Tatsuya and Chiu, Wah and Gezelle, Jeanine G. and Haack, Daniel and Hong, Yibao and Jadhav, Shekhar and Koirala, Deepak and Kretsch, Rachael C and Lewicka, Anna and Li, Shanshan and Marcia, Marco and Piccirilli, Joseph and Rudolfs, Boris and Srivastava, Yoshita and Steckelberg, Anna-Lena and Su, Zhaoming and Toor, Navtej and Wang, Liu and Yang, Zi and Zhang, Kaiming and Zou, Jian and Baker, David and Chen, Shi-Jie and Demkin, Maggie and Favor, Andrew and Hummer, Alissa M and Joshi, Chaitanya K. and Kryshtafovych, Andriy and Kucukbenli, Emine and Miao, Zhichao and Moult, John and Munley, Christian and Reade, Walter and Viel, Theo and Westhof, Eric and Zhang, Sicheng and Das, Rhiju},
+  title = {Template-based RNA structure prediction advanced through a blind code competition},
+  elocation-id = {2025.12.30.696949},
+  year = {2025},
+  doi = {10.64898/2025.12.30.696949},
+  publisher = {Cold Spring Harbor Laboratory},
+  URL = {https://www.biorxiv.org/content/early/2025/12/30/2025.12.30.696949},
+  eprint = {https://www.biorxiv.org/content/early/2025/12/30/2025.12.30.696949.full.pdf},
+  journal = {bioRxiv}
+}
+```
+
 
 ## License