# Rcsb Pdb

> RCSB PDB MCP — experimentally determined macromolecular structures.

- name: io.github.pipeworx-io/rcsb-pdb
- version: 0.1.2
- connection class: R0 (autonomous)
- trust: 97/100
- quality: –/100 (not scored)
- owner: not claimed
- descriptor: https://api.protogrid.dev/v1/servers/io.github.pipeworx-io%2Frcsb-pdb
- tools: https://api.protogrid.dev/v1/servers/io.github.pipeworx-io%2Frcsb-pdb/tools

**An agent can connect right now, no human step.** Remote endpoint, no authentication, reachable on the last probe.

## Connection (mcpServers)

```json
{
  "mcpServers": {
    "rcsb-pdb": {
      "type": "http",
      "url": "https://gateway.pipeworx.io/rcsb-pdb/mcp"
    }
  }
}
```


## Trust

- hygiene: 100
- liveness: 100
- freshness: 100
- provenance: 90
- drivers: +repository +namespace-matches-repo +website +reachable +uptime-99% +updated-24d-ago
- Derived from observable signals (official registry feed and our own credential-free probes); no code audit performed.

## Quality –/100 (not scored)

Not scored: fewer than three checks apply, usually because no remote answered a credential-free probe or the server is a local package.

### protocol: 75 (weight 25)

- warn `protocol.modern`: newest supported version is 2025-03-26; 2026-07-28 not supported, older versions are deprecated until 2027-07-28
- n/a `protocol.stateless`: only applies to 2026-07-28 servers
- pass `protocol.transport`: streamable HTTP
- n/a `protocol.list_ttl`: only applies to 2026-07-28 servers

### authorization: n/a (weight 15)

- n/a `auth.prm`, `auth.as_metadata`, `auth.cimd`: no remote uses OAuth
- n/a `auth.secret_in_url`: no templated URL

### tool hygiene: n/a (weight 30)

- n/a `tools.descriptions`, `tools.description_length`, `tools.schemas`, `tools.annotations`, `tools.directory_hints`, `tools.token_cost`, `tools.api_dump`: tool list unknown (behind auth, not probed, or empty)

### stability: n/a (weight 15)

- n/a `stability.changes`, `stability.rug_pull`: tool list unknown

### dependencies: n/a (weight 15)

- n/a `deps.known_vulns`, `deps.mcp_sdk_version`, `deps.resolvable`: no npm or PyPI package

- tools: unknown
- tools last changed: 2026-10-06T06:23:01.607Z
- badge: [![protogrid quality](https://protogrid.dev/badge/io.github.pipeworx-io/rcsb-pdb.svg)](https://protogrid.dev/servers/io.github.pipeworx-io/rcsb-pdb)
- Checks run on what our credential-free, read-only probes observe; tools are never called and no code audit is performed.

### Tool changes

- 2026-10-06 `assembly` removed
  - "Biological assembly of [pdb_id]" / "functional oligomer for [PDB entry]" — fetch a biological assembly record (the functional oligomeric unit, which often differs from the crystallographic asymmetric unit). Use when you need the actual functional form of a protein (dimer / tetramer / etc.) rather than the crystal contents.
- 2026-10-06 `polymarket_edge_tracker` removed
  - Edge persistence and decay telemetry built from daily polymarket_edges snapshots. Answers "how long has this edge existed and is it shrinking?" — a fresh wide edge and a 3-week-old wide edge are different trades (the latter is wide for a reason nobody is willing to take). Args: days (lookback, default 14, max 30), window (snapshot family, default "1wk"). RESPONSE: tracked[] = every opportunity in the LATEST snapshot with its full edge_pp_net time-series across prior snapshots, first_seen, trend (new | widening | stable | decaying) and decay_pp_per_day (both computed on |edge_pp_net| — the value itself is signed by trade direction, negative = SELL YES); expired[] = opportunities that appeared in earlier snapshots but are GONE from the latest (closed, resolved, or arbed away) with their lifespan_days — the median lifespan is your competition clock; snapshot_dates[] = which days actually have data (snapshots are written when polymarket_edges runs on a cache-miss, so gaps mean nobody scanned that day). LIMITS: history depth is bounded by the 60-day snapshot TTL and starts from when snapshotting was enabled; decay numbers come from daily closes of edge_pp_net (net of default slippage AND Polymarket's own taker fee — see polymarket_edges), not intraday.
- 2026-10-06 `polymarket_arbitrage` removed
  - Find arbitrage opportunities on Polymarket via monotonicity violations + partition-sum checks. Call with NO args for a `trending_scan` of the top ~200 markets by weekly volume; pass `event` for the strongest per-event partition_check, or `topic` for a themed cross-event scan. `event` (recommended for a specific market): pass a Polymarket event slug like "fed-decision-may-2026" or "when-will-bitcoin-hit-150k"; walks child markets, checks date-axis / threshold-axis ordering AND computes the partition_check (sum of YES prices across mutually-exclusive legs — should ≈1; deviations >3pp emit a BUY/SELL EVERY LEG signal). `topic` (for cross-event scanning): pass a seed question like "Strait of Hormuz traffic returns to normal" or "Fed rate decision"; searches related events across the platform, flattens markets, runs the comparator on the union. Cross-event mode catches "...by May 31" vs "...by Jun 30" patterns that single-event misses. SEMANTIC ANCHOR: cross-event pairs require ≥0.30 Jaccard similarity on question tokens (prevents Powell-Fed-Pause being paired with Powell-DOJ-probe); skipped_low_similarity surfaces the rejected pair count. PARTITION FILTER: drops will-person-X / will-manager-Y / will-someone-else- placeholder slugs; partitions with >20% placeholder fraction return null arb signal. Response: opportunities[] (gap_pp, suggested_trade, reasoning, monotonicity violation context), and in event mode partition_check{sum_yes_prices, gap_from_1, placeholders_filtered, suggested_trade}. FEES: every opportunities[] row and partition_check.arbitrage carry edge_pp_gross (== gap_pp / overround_pp), fees_pp, edge_pp_net, net_positive, plus polymarket_fee_pp, fee_basis and fee_categories[]. BOTH cost components are modeled: Polymarket's own per-category TAKER FEE (fee = shares × rate × p × (1-p), rates crypto 0.07 / sports-economics-culture-weather-other 0.05 / finance-politics-mentions-tech 0.04, geopolitics and world events fee-free; verified against Polymarket's own docs as of 2026-09-13) and Polygon gas (~$0.02/leg). The taker fee dominates: ~$1.75 per 100 shares on a crypto market at 50c versus $0.02 of gas, so rows that looked profitable before fleet #1927 may now show net_positive:false — that is the correction, not a regression. Each leg is priced at ITS OWN market's rate and price (the fee curve peaks at 50c and falls toward both extremes). fee_basis says where the rate came from: 'payload' (read off the market, the normal case), 'category' (mapped from its fee category), 'fee_free', or 'fallback' (rate unknown — charged at the modal 0.05 rather than assumed free, so an unreadable market is never reported as costless). Where fill_check reprices against live depth, this does NOT double-count that spread cost. FILL CHECK: when the partition signal fires, arbitrage.fill_check prices it against live CLOB depth (theoretical_edge_pp_at_book vs realizable_edge_pp at 1000 shares/leg, thin_legs[]) — realizable_edge_pp ≤ 0 means the overround exists only at last-trade, not in the book; do not trade it. For custom sizing use polymarket_fill_risk.
- 2026-10-06 `company_facts` removed
  - TYPED, DETERMINISTIC financial facts for a US public company for an EXPLICITLY NAMED reporting period — "Apple revenue for fiscal 2023", "Walmart net income FY2026 Q3", "Microsoft cash at the end of fiscal 2024". PREFER OVER entity_profile / get_company_financials whenever the period matters: those answer "the most recent figures" and will happily hand back FY2025 when you asked about FY2019, and neither separates a discrete quarter from a year-to-date figure. This one refuses instead — it NEVER substitutes the latest period for the period requested, NEVER returns 0 for missing data, NEVER lets a 9-month YTD number answer a quarterly question, and NEVER converts a currency. Every answer carries the exact us-gaap concept it came from, what that concept MEASURES (NetIncomeLoss excludes non-controlling interests, ProfitLoss includes them — not synonyms), the accession number and a link to the filing on sec.gov, the restatement trail of any superseded figures, and a contract + derivation version to pin against. Fiscal periods are the FILER'S OWN, anchored on their fiscal-year end, so Walmart's year ending 2026-01-31 is FY2026 and Apple's ending 2025-09-27 is FY2025. Attributes in v1: revenue, net_income, cash. Every non-answer is a named status — `unavailable` (the filer did not report it for that period; the periods that DO exist are listed, without values), `unsupported` (outside what v1 covers — a non-us-gaap filer, an unknown attribute, a non-USD unit), `ambiguous` (the company name matched two filers equally well; both are named), `conflicting` (two filings the same day disagree; both are returned and neither is picked), `partial` (a value with no accession behind it). Source: SEC EDGAR XBRL companyconcept, one publisher read once — see `corroboration`. Same response is served at POST https://gateway.pipeworx.io/v1/facts for non-MCP callers.
- 2026-10-06 `entity_profile` removed
  - "Tell me about X" / "research Acme" / "brief me on Tesla" / "what does Apple do" / "company profile for Microsoft" / "give me the rundown on NVDA" / "everything you know about $TICKER" — full cross-source profile of a US public company in ONE parallel call. ALWAYS PREFER over chaining single-pack SEC/XBRL/news lookups when the user asks for a holistic view. Fans out across SEC EDGAR, XBRL, USPTO patents, federal contracts (USAspending), FDA-licensed biologics (Purple Book), H-1B hiring (DOL LCA), news and GLEIF, and returns: cik + company_name (+ resolved_from/resolved_to when `value` was a name); recent_filings (up to 5 with pipeworx://edgar/company/{cik}/filings/{accession} URIs); fundamentals (LATEST 10-K Revenues + NetIncomeLoss + Cash, sorted period_end DESC); patents (USPTO PatentsView API sunset May 2025 — soft-fails until reactivated); federal_contracts (USAspending awards where the company is the recipient); fda_products (FDA-licensed biologics — vaccines, cell/gene therapies — from the Purple Book; a company with only small-molecule/generic drugs will show none here, that is expected, not a failure); hiring (H-1B sponsorship volume + salary range from DOL LCA filings); recent news mentions via GDELT→GNews fallback; LEI via GLEIF. `sources_used` / `sources_failed` say which of these actually returned data for THIS company — an empty section is a real "no data", not a bug. `sources_skipped` is the third state: a leg we deliberately did NOT run, each entry carrying a `reason` token and a plain-English `detail` (the Purple Book is skipped for a filer SEC classifies outside the life-science SIC bands, since it lists only 351(a)/(k) biologics licence holders). Pass a ticker ("AAPL"), zero-padded CIK ("0000320193"), OR a company name ("Moderna") — names now resolve via SEC EDGAR's company-name match; a private company (no CIK/ticker) returns resolved:false with an explicit `notes` line, not a bare failure. `type` accepts "company" or "ticker" interchangeably — both take the same `value` shapes above.
- 2026-10-06 `list_subscriptions` removed
  - List the caller's active subscriptions. Returns id, type, params, created_at, last_fired_at, fire_count for each. Use this to review what you're monitoring before adding more or to find an id to cancel.
- 2026-10-06 `deep_research` removed
  - ACCOUNT REQUIRED (free — sign in via GitHub at https://pipeworx.io/signup; depth:"thorough" needs a paid plan). If you are not signed in, use ask_pipeworx instead — it works on every tier. Grounded multi-source research across Pipeworx's 1685 STRUCTURED data sources (SEC filings, FRED/BLS economics, FDA, USPTO patents, markets, science, government records, etc.) in ONE call — this is NOT open-web search. Decomposes your question into focused facets, routes each to the right one of 6,475 tools IN PARALLEL, and returns a findings packet: verbatim evidence + confidence + source + fetched_at + a stable pipeworx:// citation per finding, with explicit gaps[] for facets the data couldn't answer (never invented). Best for broad/multi-part questions over structured data ("compare X and Y's regulatory + financial exposure", "research the filings + market picture for ACME"). For a single lookup use ask_pipeworx (one LLM call, not many). For BREAKING or colloquial CURRENT-NEWS / "what's the world saying about X" topics, prefer ask_pipeworx — it routes to live news APIs and the *-news-feeds packs; deep_research returns mostly empty gaps[] when the topic isn't in the structured catalog. Second-hop iteration: depth:"standard" re-angles unanswered gaps (gap recovery); depth:"thorough" additionally chases the best leads from the first pass — so multi-step questions resolve in one call. Every finding carries a `hop` field and a citation_uri — a resolvable pipeworx:// record URI, present only when the source emits one that resources/read can actually serve, so a citation you get back is always fetchable. "standard" and "thorough" also return contradictions[] flagging findings that disagree. Large records are semantically excerpted to the passages relevant to each facet (not head-truncated), so answers deep in a long filing/series aren't missed. Expect 15-60s (thorough with its follow-up + contradiction pass: up to ~90s).
- 2026-10-06 `forget` removed
  - Delete a previously stored memory by key. Use when context is stale, the task is done, or you want to clear sensitive data the agent saved earlier. Pair with remember and recall.
- 2026-10-06 `resolution_audit` removed
  - Extract the settlement clause of a single Polymarket or Kalshi market: who publishes the settling number (source), the clock time + timezone it is taken at, the precision of the computation (e.g. "1-minute candle close" vs "60-second trailing average" vs "election outcome"), the evidence standard (official_source | consensus_reporting | any_credible_report | unspecified), and void_handling (cancellation/postponement settlement — reused verbatim from bet_research's cancellation_rule detector, not re-derived). Parses Polymarket's `description` field (fetched via polymarket_market) or Kalshi's `rules_primary` + `rules_secondary` fields (fetched via kalshi_market) with regex + a small vocabulary — no LLM pass, so an unusual clause reports confidence:"low" rather than a guess. Pass `market` as a Polymarket slug/URL or a Kalshi market ticker (e.g. "KXBTCD-26SEP1317-T66999.99"); a Kalshi EVENT ticker (e.g. "KXBTCD-26SEP1317") also works — it picks one representative market under that event, since the settlement mechanism is normally shared across all strikes/legs in one event. Use this before treating a polymarket_kalshi_spread row as a real arbitrage: two ladders that look alike can settle on different sources, at different times, with different precision — this tool is how you check. Pair with resolution_diff to compare two markets directly. KNOWN GAP: idiosyncratic phrasing that doesn't match the vocabulary returns confidence:"low" and evidence_standard:"unspecified" rather than an LLM-guessed answer.
- 2026-10-06 `polymarket_fill_risk` removed
  - Realizable-vs-theoretical edge check against live CLOB order-book depth. REQUIRES one of `market` (single-market mode) or `event` (basket/partition mode). SINGLE-MARKET: pass a market slug/URL + side (buy_yes|sell_yes|buy_no|sell_no, default buy_yes) + size_usd (default 1000 — max spend on buys, target proceeds on sells); walks the ladder and returns top_of_book, vwap_fill_price, slippage_pp, shares_filled, max_fillable_usd, and a verdict (clean|degraded|cannot_fill). BASKET: pass an event slug/URL + side (sell_yes = capture overround by selling every leg, buy_yes = capture underround; default auto from partition sum) + size_usd interpreted as settlement notional S (shares per leg; each share pays $1); returns theoretical_sum vs realizable_sum (top-of-book vs VWAP across all legs), capture_ratio, profit_usd at executed size, per-leg fill detail, thin_legs[], max_clean_notional_usd, and forced_directional_risk naming the legs most likely to strand you unhedged. USE THIS before acting on any polymarket_arbitrage SELL/BUY-EVERY-LEG signal or any polymarket_edges trade above ~$500 — theoretical overround on thin books is not capturable, and partial basket fills convert an arb into an unhedged directional position (the dominant loss mode in real arb-bot P&L). FEES ARE NOT MODELLED HERE: vwap_fill_price/profit_usd are GROSS of Polymarket's own taker fee (rate 0.04-0.07 by category — see polymarket_edges/fees.ts), on top of which this tool prices depth-crossing cost; a thin-margin fill that looks clean here can still be net-negative after the fee.

Full history: https://api.protogrid.dev/v1/servers/io.github.pipeworx-io%2Frcsb-pdb/changes

## Remotes

- https://gateway.pipeworx.io/rcsb-pdb/mcp (streamable-http, auth none, reachable true, uptime30d 0.99159664)

## Packages

_none_

## Tools (0)

_none observed_