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Rcsb Pdb

by io.github.pipeworx-io
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RCSB PDB MCP — experimentally determined macromolecular structures.

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Status
Unhealthy
Last Tested
Transport
Streamable HTTP
URL
Repository
pipeworx-io/mcp-rcsb-pdb
GitHub Stars
0
Server Listing
mcp-rcsb-pdb

TDQS

A3.8/5.0

Scored across 37 tools

Disambiguation2/5

There is substantial overlap among the router/meta tools: ask_pipeworx, ask_pipeworx_beta (explicitly stated to currently match ask_pipeworx), ask_pipeworx_grounded, and deep_research all answer questions over the same 5,961-tool catalog, and entity_profile/compare_entities/recent_changes/validate_claim also heavily overlap on entity research. The detailed descriptions help but cannot fully resolve boundaries an agent must guess between.

Naming Consistency4/5

Names are uniformly snake_case, with no camelCase or chaotic mixing. The only inconsistency is verb style — some are verb_noun (list_subscriptions, resolve_entity, validate_claim) while others are bare nouns (structure, summary, ligand) — but the convention remains predictable.

Tool Count2/5

37 tools is very heavy for the advertised RCSB PDB scope, which needs only ~6 tools. The bulk of the surface (LLM-visibility, Polymarket, memory, subscriptions, dependency scanning) is unrelated to the server name, making the count feel bloated and mismatched.

Completeness4/5

For the PDB domain the six tools (search, structure, summary, assembly, ligand, polymer_entity) cover the core entry/entity/ligand lifecycle well. Minor gaps exist (no sequence/chemical-component search), but the primary structural-biology workflows are covered.

Tool Schema Changelog

Recent tool additions, removals, and schema changes observed during successful MCP inspections.

  1. 2 tool updates
    • Changedbet_research2 fields changed
      • changedInput schema / examples
        Previous value: -[
-  {
-    "market": "when-will-bitcoin-hit-150k"
-  },
-  {
-    "market": "https://polymarket.com/event/when-will-bitcoin-hit-150k"
-  }
-]New value: +[
+  {
+    "market": "will-kristi-noem-win-the-2028-republican-presidential-nomination"
+  },
+  {
+    "market": "https://polymarket.com/event/will-kristi-noem-win-the-2028-republican-presidential-nomination"
+  }
+]
      • changedInput schema / properties / market / description
        Previous value: -"Polymarket slug (\"when-will-bitcoin-hit-150k\"), full URL (\"https://polymarket.com/event/...\"), or question text (\"Will Bitcoin hit $150k?\"). Dated slugs stop resolving once they settle — Polymarket de-indexes resolved markets — so prefer an undated one."New value: +"Polymarket slug (\"will-kristi-noem-win-the-2028-republican-presidential-nomination\"), full URL (\"https://polymarket.com/event/...\"), or question text (\"Will Bitcoin hit $150k?\"). Dated slugs stop resolving once they settle — Polymarket de-indexes resolved markets — so prefer an undated one."
    • Changedpolymarket_kalshi_spread1 field changed
      • changedInput schema / examples
        Previous value: -[
-  {
-    "topic": "fed"
-  },
-  {
-    "topic": "btc"
-  }
-]New value: +[
+  {
+    "topic": "fed"
+  },
+  {
+    "topic": "btc"
+  },
+  {
+    "topic": "bitcoin"
+  },
+  {
+    "topic": "fed rate decision"
+  }
+]
  2. 2 tool updates
    • Changedbet_research2 fields changed
      • changedInput schema / examples
        Previous value: -[
-  {
-    "market": "will-bitcoin-reach-100k-in-july-2026"
-  },
-  {
-    "market": "https://polymarket.com/event/will-bitcoin-hit-150k-by-june-30-2026"
-  }
-]New value: +[
+  {
+    "market": "when-will-bitcoin-hit-150k"
+  },
+  {
+    "market": "https://polymarket.com/event/when-will-bitcoin-hit-150k"
+  }
+]
      • changedInput schema / properties / market / description
        Previous value: -"Polymarket slug (\"will-bitcoin-hit-150k-by-june-30-2026\"), full URL (\"https://polymarket.com/event/...\"), or question text (\"Will Bitcoin hit $150k by June 30?\")"New value: +"Polymarket slug (\"when-will-bitcoin-hit-150k\"), full URL (\"https://polymarket.com/event/...\"), or question text (\"Will Bitcoin hit $150k?\"). Dated slugs stop resolving once they settle — Polymarket de-indexes resolved markets — so prefer an undated one."
    • Changedpolymarket_kalshi_spread1 field changed
      • changedInput schema / properties / topic / description
        Previous value: -"Pre-mapped: fed | btc | cpi | gdp | sp500 | recession | next_pope | next_uk_pm | next_israel_pm | 2028_president"New value: +"Subject to compare. Canonical keys: fed | btc | eth | cpi | gdp | sp500 | recession | next_pope | next_uk_pm | next_israel_pm | 2028_president — but aliases and keywords resolve too (\"bitcoin\", \"fed rate decision\", \"ethereum\", \"inflation\", \"s&p 500\", \"us recession\", \"next pope\", \"2028 election\"). Check resolution.topic_matched_by in the response: \"exact\"/\"alias\" is a curated pairing, \"phrase\"/\"token\" is a keyword guess."

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