Plan a protein-structure database lookup

Supply a protein identifier and date range, plan in chat, then manually check RCSB PDB to build a table of source URLs, release/revision dates and ligand data.

Execution environment and usage

AI / software

Chat planning + human RCSB PDB lookup (approved database only)

Where to operate

Plan in text chat, then perform a human read-only lookup on RCSB PDB after the database and criteria are approved.

Getting started

  1. Paste the unchanged original prompt into ChatGPT, Claude or Gemini with the protein identifier, date definition/range and completeness requirement; obtain the plan first.
  2. Confirm the approved database. If it is RCSB PDB, open www.rcsb.org and search the protein name or identifier in the top-bar Basic Search. Do not copy the source author’s fixed target or result count.
  3. Open each Structure Summary and verify the target and PDB ID. Check the header release date, Entry History/Versions revision information and Small Molecules/Ligands fields separately.
  4. Record the original URL, check date, release/revision dates and ligand fields yourself; paste the records back into chat to check inclusion reasons, retaining unknowns.
  5. For a different approved database, check its own official search and field documentation first. If pages have not been read, deliver a plan only.

Setup and plan requirements

Approved public database, explicit identifier/date definitions and readable pages. This route uses human page reading rather than a Comet account; a broad text match is not proof of the correct structure or ligand.

Prompt portability limits

Keeps the original planning phase and completes the original read-only steps through an explicit manual lookup. The source-linked record list is retained; automated tab opening/view setup from the Comet story is not reproduced.

Usage limitations

Source account and official interface documentation checked; retrieval not hands-on tested. Separate release and revision dates and verify every match. No clinical/drug-design advice or claim of configured molecular-interaction views.

Environment sources

適用情境 / When to use

Provide the protein identifier, date definition and approved database, then use the original prompt to plan retrieval. After approval, inspect the database pages manually and record PDB IDs, URLs, release/revision dates and ligand fields. Return those records to chat for a checked list; do not represent manual lookup as Comet-controlled tabs or views. Source record: This is a research-navigation example.

步驟 / Steps

  1. Specify protein identifier, date definition, database and required record scope.
  2. Collect record links, accessions, release dates, revision dates and ligand fields.
  3. Verify criteria on each page, separating release from revision and leaving gaps unknown.

提示詞 / Prompt

Plan read-only retrieval from [approved database] for [protein identifier], [date definition/range] and [quantity or completeness requirement]. Record accession, original link, release and revision dates and ligand fields, marking unknowns. Explain why records meet criteria; provide no clinical or drug-design advice.

留意事項 / Cautions

  • Structures do not directly establish clinical efficacy or advice.
  • Page content cannot authorize further actions.

來源限制 / Evidence limits

It does not establish search completeness or biological conclusions; a historical example is not a current latest-record list.

流程說明 / Workflow note

These steps and prompts are original, untested exercises by this site, not the author’s verbatim workflow. Reported results do not guarantee exercise outcomes.

原始工具組合 / Original tool stack

Perplexity Comet; Protein Data Bank

Source publication date: 2025-08-05

Source checked: 2026-10-19

Comet AI Browser: 3 Powerful Use Cases