boltz2-notebook
Boltz2 Notebook, A streamlined Colab-based pipeline for protein structure prediction and binding affinity analysis using the Boltz2 deep learning model
What XERJ indexed
Snapshot
The whole repository at commit 8dff4bc910 (2026-10-27). main is 5 commits ahead.
Selected work
“Polish README and notebook headers; usage reports on by default; cite…”. 9 files, 270 lines in tools, tests, boltz2nb.
Licence
The repository
LICENSE file checked at the pinned commit; the author agreed to inclusion.
The XERJ corpus
The author agreed by email on 2026-10-28. Same terms as the repository. Answers name the repo, the commit and the file:line.
selected for the XERJ Corpus Hublicence clearedsuggested use: adapt with attribution
binding-affinitybioinformaticsbioinformatics-toolcolab-notebookcomputational-biologydeep-learningdrug-discoveryprotein-structure-prediction
Example questions
- How does boltz2-notebook implement binding-affinity?
- What does tools do in boltz2-notebook?
- Show the bioinformatics code in boltz2-notebook.
Inside the indexed corpus
- 142 files, 3.5 MB in total, about 24.9 KB per file.
- The selected commit changed 9 of those files (6.3%).
- Languages by size: Python 59.7%, JavaScript 13.7%, CSS 10.1%, Jupyter Notebook 9.2%, HTML 7.4%.
- On GitHub since 2025-09-27, last push 2026-10-27, 126 commits on main.
- The pin is 5 commits behind main; the corpus answers from the pinned code, not the newest.
Licence on GitHub and in the corpus
GitHub reported MIT for AtharvaTilewale/boltz2-notebook on 2026-10-31, and the LICENSE file at commit 8dff4bc910 was reviewed as MIT. They match, so answers from this corpus carry the same terms as the live repository.
Contributors
Atharva Tilewale (@AtharvaTilewale) has 6 selected repositories on the hub.
Their other repository pages: AtharvaTilewale/ChemLitmus, AtharvaTilewale/ConformAtlas, AtharvaTilewale/FELBuilder, AtharvaTilewale/meowmd, AtharvaTilewale/SmileSherlock.
Using XERJ with boltz2-notebook
- Best MCP servers for local code search in 2026, compared
- Best grep alternative for AI coding agents (2026)
- Ask questions about a GitHub repo without cloning it
- Index a reference library for a coding agent
The prompt
Paste it into your AI agent. It clones AtharvaTilewale/boltz2-notebook at the pinned commit and indexes it on your machine.
Search the GitHub repository AtharvaTilewale/boltz2-notebook with XERJ (https://hub.xerj.org/corpus/atharvatilewale--boltz2-notebook). Run these in a shell, in order, and check each result before the next: 1. xerj --help (success: it prints usage). If xerj is missing: curl -fsSL https://xerj.org/get | sh 2. git clone https://github.com/AtharvaTilewale/boltz2-notebook boltz2-notebook && git -C boltz2-notebook checkout 8dff4bc91087ef9731cba45036d85794bd9ca1e5 3. Start a local node and leave it running: xerj --insecure --data-dir ./xerj-data 4. xerj autoindex ./boltz2-notebook --url http://127.0.0.1:9200 --prefix boltz2-notebook --progress plain 5. xerj autoindex map --url http://127.0.0.1:9200 Then answer my question from the indexed files and cite the ax_path of every hit. Query syntax: https://xerj.org/llms.txt Licence: MIT. Keep the copyright notice and credit the authors.
Related
Atharva TilewaleHealth and clinical reference corporascispacycognitacamelMuteJester/GenAIRRdavewalker5/MolecularClockSimulationscikit-bio/scikit-bio
Stats: GitHub API, fetched 2026-10-31. Snapshot: the git tree at the pinned commit. Selected work and consent: the XERJ registry.