Search / io.github.pipeworx-io/pdbe
Pdbe
R0· no sign-inPDBe (Protein Data Bank in Europe, EBI) MCP.
v0.1.2 · active · repository · website · descriptor JSON · versions
Search / io.github.pipeworx-io/pdbe
R0· no sign-inPDBe (Protein Data Bank in Europe, EBI) MCP.
v0.1.2 · active · repository · website · descriptor JSON · versions
{
"mcpServers": {
"pdbe": {
"type": "http",
"url": "https://gateway.pipeworx.io/pdbe/mcp"
}
}
}claude mcp add --transport http pdbe https://gateway.pipeworx.io/pdbe/mcp[mcp_servers.pdbe]
url = "https://gateway.pipeworx.io/pdbe/mcp"
{
"$schema": "https://opencode.ai/config.json",
"mcp": {
"pdbe": {
"type": "remote",
"url": "https://gateway.pipeworx.io/pdbe/mcp",
"enabled": true
}
}
}{
"mcpServers": {
"pdbe": {
"type": "http",
"url": "https://gateway.pipeworx.io/pdbe/mcp"
}
},
"deeplink": "cursor://anysphere.cursor-deeplink/mcp/install?name=pdbe&config=eyJ0eXBlIjoiaHR0cCIsInVybCI6Imh0dHBzOi8vZ2F0ZXdheS5waXBld29yeC5pby9wZGJlL21jcCJ9"
}{
"servers": {
"pdbe": {
"type": "http",
"url": "https://gateway.pipeworx.io/pdbe/mcp"
}
}
}{
"mcpServers": {
"pdbe": {
"httpUrl": "https://gateway.pipeworx.io/pdbe/mcp"
}
}
}extensions:
"pdbe":
enabled: true
name: "pdbe"
type: streamable_http
uri: "https://gateway.pipeworx.io/pdbe/mcp"
timeout: 300
Not scored: fewer than three checks apply, usually because no remote answered a credential-free probe or the server is a local package.
protocol.modernnewest supported version is 2025-03-26; 2026-07-28 not supported, older versions are deprecated until 2027-07-28protocol.statelessonly applies to 2026-07-28 serversprotocol.transportstreamable HTTPprotocol.list_ttlonly applies to 2026-07-28 serversauth.prm, auth.as_metadata, auth.cimdno remote uses OAuthauth.secret_in_urlno templated URLtools.descriptions, tools.description_length, tools.schemas, tools.annotations, tools.directory_hints, tools.token_cost, tools.api_dumptool list unknown (behind auth, not probed, or empty)stability.changes, stability.rug_pulltool list unknowndeps.known_vulns, deps.mcp_sdk_version, deps.resolvableno npm or PyPI packageforgetremovedDelete 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.
recent_alertsremovedPull fired events from your subscription feed. Returns the most recent alerts the evaluator has written to your persisted feed — each carries source, citation_uri (pipeworx:// when available), and the raw event payload. Filter by type (e.g. "sec_8k") and/or since (ISO timestamp). Set mark_read:true to flag returned events read so the next call only shows newer ones. Polls work fine; the same feed is also at GET registry.pipeworx.io/alerts.json for scripts and dashboards.
get_moleculesremovedPDBe (EBI): list the molecules/entities in a PDB structure — proteins, nucleic acids, and ligands, each with entity_id, molecule_type, name, and chain length. Keyless. Pass a 4-char PDB id like "1cbs".
scan_competitor_ai_presenceremovedCompare AI visibility across multiple entities side-by-side. Probes each entity (your brand + N competitors) with ai_visibility_check, ranks by score, surfaces which is most/least recognized. Useful for competitive AI-marketing audits: "does Claude know about us as well as our competitors?". Returns ranked list with score, confidence, signal density per entity.
list_subscriptionsremovedList 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.
polymarket_kalshi_spreadremovedCross-venue spread between Kalshi and Polymarket for the same resolving question. The two venues sometimes price the same outcome 2-25pp apart because their participant pools differ — when the bet shapes are equivalent that delta is a real signal, when they aren't the tool says so. TWO MODES: (1) `topic` — 11 pre-mapped macro subjects ("fed", "btc", "eth", "cpi", "gdp", "sp500", "recession", "next_pope", "next_uk_pm", "next_israel_pm", "2028_president") auto-fetch the matching event on each venue. You do NOT have to use those exact keys: the topic is resolved through aliases and keywords, so "bitcoin", "fed rate decision", "inflation", "s&p 500" and "next pope" all land on the right subject, and `resolution.topic_matched_by` tells you whether it was an exact key, a known alias, a phrase found inside a longer question, or a single-keyword guess — treat "phrase" and "token" as a GUESS at what you meant. An unresolvable topic returns error:"mapping_failed" with mapping_stage:"topic_unrecognized" and known_topics[]; it never silently falls back to a default subject. (2) explicit `kalshi_event_ticker` + `polymarket_event_slug` for custom pairings — BOTH modes run the identical token-overlap matcher, so the same disclosures apply to both. `resolution` is returned in BOTH modes and says how each side's identifier was picked (which Kalshi series was queried, how many events came back, whether the chosen one had quoted markets; which Polymarket search query ran and why that event won). Fleet #2064: when two Polymarket candidates tie on resolution time `polymarket_selected_by` now SAYS so, names every tied slug, names the tie-break that actually decided it (the candidate whose metric_type matches the Kalshi series, else lexicographic slug order), and states whether the winner's metric matches the Kalshi series — it used to assert "picked the soonest-resolving" byte-identically on calls that returned DIFFERENT events, because the tie was settled by upstream fetch arrival order. RESPONSE: each venue's leg-by-leg prices (raw probability 0-1) plus matched spread[].top_spreads_pp (Kalshi − Polymarket) where the same outcome shows up on both sides. SAFETY FIELDS: compatibility_warning is a sentence and compatibility_codes[] the machine-readable form; BOTH can be non-empty on returned pairs, so read them even when matched_pairs>0. Codes: event_subject_mismatch (the two event titles share no subject words — probably not the same question), temporal_mismatch (the two events are about different SUBJECT months — e.g. Kalshi "CPI in October" vs Polymarket "September Inflation"), temporal_alignment_unknown (the subject month could not be parsed on one or both sides — NOT the same as confirmed-aligned; check each event yourself), non_equivalent_bet_shapes, no_candidate_pairs, unclassified_legs_excluded, pairing_unverified (set in EITHER mode whenever pairs are returned: the legs were matched by keyword and word overlap, not a shared resolution source). Each entry in top_spreads_pp carries its own flags[] (temporal_mismatch, temporal_alignment_unknown, event_subject_mismatch, low_token_overlap). A leg whose metric_type or match_subtype is "unknown" is NEVER paired — those comparisons land in spread.skipped_unclassified and, when the wording lined up, in spread.low_confidence_pairs[] for inspection only. temporal_alignment{polymarket_month,kalshi_month,aligned} tells you whether the two events are about the same SUBJECT calendar period, in EITHER mode — this is the period the question is ABOUT (e.g. "September" for a CPI release that settles in October), not necessarily when either side settles; null means it could not be computed (see temporal_alignment_unknown), not that the two sides align. Fleet #2062: this used to compare Polymarket's settlement date against Kalshi's subject month and call a match — fixed to compare subject month to subject month on both sides. FEES: every top_spreads_pp and low_confidence_pairs[] row carries edge_pp_gross (== |sp
polymarket_edge_trackerremovedEdge 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.
bet_researchremovedResearch a Polymarket bet by pulling the relevant Pipeworx data for it in one call. Pass a market slug ("will-kristi-noem-win-the-2028-republican-presidential-nomination"), a polymarket.com URL, or a question text. Prefer an UNDATED slug: a dated one ("...-by-june-30-2026") stops resolving the day it settles, because Polymarket de-indexes resolved markets. The tool resolves the market, classifies the bet, fans out to category-specific data packs in parallel, and returns an evidence packet + simple market-vs-model comparison. Use for "should I bet on X", "what does the data say about Y", or "is there edge in Z". CLASSIFIERS: crypto_price, fed_rate, geopolitical, sports, sports_championship, drug_approval, election_candidate, tech_launch, space_launch, corporate, corporate_earnings, corporate_event, public_figure_speech, weather, other. FAN-OUT EXAMPLES: BTC bet → coingecko + fred + gdelt+gnews; Fed bet → fred (DFEDTARU + EFFR + CPIAUCSL) + kalshi_macro (KXFED implied probs) + recent_fed_actions (federal-register rules, last 365d); Hormuz bet → imf_portwatch + airspace + gdelt; Yankees WS → mlb_stats_standings + parent_event partition + news; hottest-year bet → climate_projection_nyc + gistemp_latest (NASA global anomaly, rank since 1880) + news; NVDA-vs-AAPL → finnhub get_quote + edgar shares-outstanding (derived market cap) + edgar filings + news. RESPONSE SHAPES: result.market carries best_bid/best_ask/spread_pp/liquidity/price_change_1h/1d/1w; result.analysis carries model_probability/edge_pp/kelly_fraction_half when a closed-form model fires PLUS a 24h-move warning ("Market moved X.Xpp in 24h, comparable to model edge — your edge may already be priced in") when relevant; result.evidence is keyed by source. RESOLVER CONTRACT: result.market_match_confidence ∈ {high, medium, low, none}, market_match_score (0-1 token-overlap), market_match_alternatives[] (other candidate markets the resolver considered), and suggestions[] (explicit re-query hints when the match is fuzzy) — ALWAYS inspect these before trusting the analysis block, because medium/low matches can still surface other fields. PARENT_EVENT EXTRACTOR: when the bet is one leg of a partition (Yankees WS, Romania election), result.parent_event{matched_candidate, top_legs_by_price[], partition_size, placeholders_filtered} gives you the peer prices in one place — that's the headline for elections/championships. NEWS FIELDS: news entries carry _fallback_attempted / _fallback_failed_reason / retry_after_sec when GDELT 429s and GNews backfill ran or failed. SAFETY: low-confidence resolutions short-circuit with status:"low_confidence_match" and suppress analysis fields so agents can't accidentally size on phantom matches. Closed/dead markets that ARE still indexed by Polymarket (yes_price≈0, no volume, no liquidity) return status:"market_closed_or_inactive" and skip fan-out. A market whose own deadline has already passed returns status:"market_expired_or_resolved" + expired_deadline (the date), which is deliberately NOT the same answer as low_confidence_match: your slug was right and is merely settled, so the useful retry is the successor market for the same question, not a corrected spelling. In practice resolved markets are usually de-indexed and instead surface via one of those two paths — both routes are BLOCKING, just different mechanisms. Wide-spread markets (>10pp) carry tradeability:"illiquid_wide_spread" + an explanatory note. RESOLUTION-RULE RISK: market.cancellation_rule parses the void/postponement settlement out of the resolution text — refund_50_50 (shares settle flat 50¢ on void; EV-material for any entry away from 50¢, with ev_impact quantified), resolves_no_on_cancel, resolves_yes_on_cancel, carries_to_reschedule, or mentioned_unclear. null means the description never mentions cancellation. Check this before sizing sports/esports/event-occurrence bets — audited arb-bot ledgers show flat-50¢ void settlements are a recurring pure-rules loss.
unsubscriberemovedCancel a subscription by id. Ownership is enforced — you can only cancel your own subscriptions. The row is deactivated (not deleted) so its historical events stay available via recent_alerts.
archive_compareremovedWhat changed on a web page between two dates? Resolves the archived capture nearest each date (Internet Archive Wayback Machine, Common Crawl, Arquivo.pt), extracts the readable text of both, and returns a text-level diff: the segments removed and added, a similarity score, and both capture timestamps with their gaps from the requested dates. It diffs readable text, not markup, so a restyled page with the same words reads changed:false. Identical captures answer changed:false with the reason (same capture, identical content digest, or identical text), never an empty diff. A date with no capture within max_gap_days (default 30) answers status "no_capture", naming which side is missing and the nearest captures to it. Typical uses: how a privacy policy, terms of service, pricing or product page changed; whether a statement was on a page at a given time.
Showing the latest 10. Full history: list_changes · trend: quality JSON.
Checks run on what our credential-free, read-only probes observe; tools are never called and no code audit is performed. How it is computed.
+repository +namespace-matches-repo +website +reachable +uptime-99% +updated-23d-ago
Derived from observable signals (official registry feed and our own credential-free probes); no code audit performed. How it is computed.
| remote | auth | reachable | uptime 30d | p50 | protocol | last ok |
|---|---|---|---|---|---|---|
https://gateway.pipeworx.io/pdbe/mcp streamable-http | none | yes | 99% | 33 ms | 2025-03-26 | 2026-10-19 |
No tools observed. Tools appear once a credential-free probe can list them.
Schemas: list_tools.
And 1,847 more from this publisher.
{
"name": "io.github.pipeworx-io/pdbe",
"title": "Pdbe",
"$schema": "https://static.modelcontextprotocol.io/schemas/2025-12-11/server.schema.json",
"remotes": [
{
"url": "https://gateway.pipeworx.io/pdbe/mcp",
"type": "streamable-http"
}
],
"version": "0.1.2",
"repository": {
"url": "https://github.com/pipeworx-io/mcp-pdbe",
"source": "github"
},
"websiteUrl": "https://pipeworx.io/packs/pdbe",
"description": "PDBe (Protein Data Bank in Europe, EBI) MCP."
}