# Bindingdb

> BindingDB — measured protein/small-molecule binding affinities.

- name: io.github.pipeworx-io/bindingdb
- version: 0.1.2
- connection class: R0 (autonomous)
- trust: 96/100
- quality: –/100 (not scored)
- owner: not claimed
- descriptor: https://api.protogrid.dev/v1/servers/io.github.pipeworx-io%2Fbindingdb
- tools: https://api.protogrid.dev/v1/servers/io.github.pipeworx-io%2Fbindingdb/tools

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

## Connection (mcpServers)

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


## Trust

- hygiene: 100
- liveness: 98
- freshness: 100
- provenance: 90
- drivers: +repository +namespace-matches-repo +website +reachable +uptime-96% +updated-0d-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: 2026-10-20T06:42:03.854Z
- badge: [![protogrid quality](https://protogrid.dev/badge/io.github.pipeworx-io/bindingdb.svg)](https://protogrid.dev/servers/io.github.pipeworx-io/bindingdb)
- Checks run on what our credential-free, read-only probes observe; tools are never called and no code audit is performed.

### Tool changes

- 2026-10-20 `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.
- 2026-10-20 `polymarket_edges` removed
  - Scan top Polymarket markets and return opportunities where Pipeworx data disagrees with market price. Built for "what should I bet on today" — agents discover opportunities without paging hundreds of markets. FIVE MODEL FAMILIES grouped into three response segments under by_segment: (1) MODEL_DRIVEN — crypto_price (lognormal barrier from 90d FRED log-returns) and news_momentum (GDELT 7d/21d article-volume ratio, soft signal w/ halved Kelly). (2) STRUCTURAL_ARBITRAGE — partition_overround on mutually-exclusive events; per-leg favorite-longshot bias correction with per-sport α (tennis 1.02, soccer 1.10, MMA 1.15, default 1.0); placeholder-slug filter drops will-person-X / will-team-Y / will-manager-Z / will-someone-else- backstops; partitions with >20% placeholder fraction skipped entirely. (3) CONCENTRATED_LONGSHOT — basket trade when one leg ≥75% AND ≥2 longshots ≤8% AND portfolio return ≥25:1; rare-by-design (gates relaxed Run 8 from prior 85%/5%/50:1). EVERY OPPORTUNITY carries edge_pp_net (net of slippage AND Polymarket's own taker fee — fees_pp_applied itemises the fee component; see fees.ts for the published per-category schedule), kelly_fraction + kelly_fraction_half (capped at 0.25), market.liquidity, market.spread_pp, market.volume, plus a 24h-move warning ("Market moved X.Xpp in 24h") when the recent move alone exceeds the edge — your edge may already be in the price. TRADEABLE-EDGE KNOBS: min_liquidity / max_spread_pp drop opportunities where edge isn't realizable; min_partition_leg_kelly filters partitions by best per-leg Kelly. RESPONSE TOP-LEVEL: by_segment{model_driven,structural_arbitrage,concentrated_longshot}, fed_candidates/fed_note (Fed bets surface here, excluded from ranking — 1m-T vs EFFR signal is unreliable at meeting-month horizons without paid OIS/SOFR-futures data), and _diagnostics{concentrated_longshot:{...funnel counters},category_counts,filter_skips} so callers can see WHY a segment is empty (top-N stale, all candidates failed gates, knob dropped them). Cached 1h at the KV level keyed on all knobs.
- 2026-10-20 `resolve_entity` removed
  - "What's the ticker for…" / "find the CIK for…" / "what's the LEI for…" / "what's the RxCUI for…" / "look up the ID for…" / "what is X's official identifier" / "who owns X" / "is X a subsidiary of Y" — resolve a user-spoken NAME to the canonical/official identifiers other tools require as input. Use FIRST whenever you have a name but need an ID. SUPPORTED TYPES: "company" (cross-source identity spine: 10-digit CIK + ticker + company_name from SEC EDGAR, legal-entity LEI from GLEIF with parent/ultimate-parent/children ownership when the LEI resolves, and security FIGI from OpenFIGI — by exact ticker map when a ticker is implied, and otherwise by name search, so NON-EQUITY instruments that never have a ticker (municipal and corporate bonds, notes, authority debt) DO resolve here; when a name matches more than one instrument it asserts nothing and returns `figi_candidates` to pick from, which is the correct answer to an issuer name that does not identify a single bond; every identifier is labelled with the source that established it, and an identifier that could NOT be resolved is stated explicitly under `unresolved` rather than omitted — accepts ticker, CIK, ISIN, or company name as input; an ISIN like "CH0038863350" resolves to the LEGAL ENTITY that issued the security via the GLEIF ISIN-to-LEI mapping, covering non-US issuers EDGAR cannot reach), "drug" (returns RxCUI + ingredient + brand from RxNorm + pipeworx://rxnorm/concept/{rxcui} citation; accepts brand or generic name). LEI/FIGI enrichment degrades gracefully — if GLEIF or OpenFIGI is unavailable, the EDGAR identifiers still return. Each call cascades through several lookup endpoints internally — using resolve_entity replaces 2-3 manual lookups.
- 2026-10-20 `validate_claim` removed
  - "Is it true that…" / "fact check" / "verify the claim that…" / "did X really…" / "was Y actually…" / "confirm or refute" / "true or false" — natural-language claim verification against authoritative sources. Use whenever the agent needs to check whether something a user said is factually correct. Company-financial claims (revenue, net income, cash for public US companies) verify via the structured SEC EDGAR + XBRL fast path with exact percent-delta math; ANY OTHER factual claim (macro statistics, rates, prices, drug data, records) automatically falls through to the grounded pipeline — routed to the right live source, answered with verbatim evidence, then judged. Returns a verdict (confirmed / approximately_correct / refuted / inconclusive / unsupported / could_not_verify), the grounded or structured actual value with pipeworx:// citation, and reasoning. IMPORTANT for callers: could_not_verify means the check did not happen (our LLM or source failed) and carries verification_error{stage,detail} — it is NOT evidence for or against the claim, and must not be shown as one. unsupported means we looked and cover no source for it. Replaces 4–6 sequential calls (NL parsing → entity resolution → data lookup → comparison).
- 2026-10-20 `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.
- 2026-10-20 `generate_llms_txt` removed
  - Generate a production-ready llms.txt file for any URL so AI crawlers (ChatGPT, Claude, Perplexity) can index the site cleanly. Fetches the page, extracts title/description/key links, and emits the standard llms.txt markdown format. Output is a single text blob ready to drop at site-root/llms.txt. Useful for: getting a client's site indexed by AI, drafting llms.txt for your own project, or auditing how an AI crawler would see a competitor.
- 2026-10-20 `pipeworx_trending` removed
  - What other AI agents are calling on Pipeworx right now. Returns the top tools, top packs, and total call volume over a recent window (24h, 7d, or 30d). Useful for: (1) discovering what data sources are hot for current events, (2) confirming a popular tool is the canonical choice before asking your own question, (3) seeing whether your use case aligns with what most agents need. Self-aggregating signal — derived from CF analytics-engine, no PII, just (pack, tool, count). Cached 5min-1h depending on window.
- 2026-10-20 `research_row` removed
  - Claygent-style per-row research: answer ONE question about ONE company and return a JSON object matching your output_schema, with every field wrapped in its own evidence — {value, evidence_url, quote, status}. status is NEVER self-reported by the model: "found" means this code independently verified the model's quote is a VERBATIM substring of text actually fetched; "inferred" means a value was given but the quote could not be verified; "not_established" means no source answered the field, and its value is always null — never guessed, never a blended score. Sources: "web" fetches the company's own site (entity.domain required — homepage, /about, /leadership) via fetch_url; "catalog" checks entity_profile (SEC EDGAR; resolved:false for a private company is expected, not a failure); "both" (default) tries both. max_cost (USD, default 0.02, max 0.50) scales how many pages are fetched and refuses up front if it is too small to pay for even one extraction call (floor $0.002) — never silently overspends. A row where every source comes back empty costs nothing: every field is mechanically not_established with NO model call made. For a boolean/derived field (e.g. "does this company sell to healthcare"), the quote only has to SUPPORT the value — a descriptive sentence about customers/products counts, the source need not state the answer verbatim. leadership_page_status ("fetched"|"not_found"|"not_attempted", plus leadership_note) says plainly whether a leadership/team page was actually read, so a named-person field (head_of_sales) coming back not_established is distinguishable from "this company just doesn't publish one" vs. "we never checked". model_output_empty:true means the model returned nothing usable (a transport/budget problem) — every field is not_established for THAT reason, never read as 20 individual "no" judgments. Use with a fixed question + schema across many rows for "Claygent over N companies with a hard cost cap" (composes with batch callers). For picking from a fixed label list instead of extracting open fields, use classify_row (cheaper, one model call).
- 2026-10-20 `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.
- 2026-10-20 `suggest_questions` removed
  - What can I ask Pipeworx? / what is Pipeworx good for? / what can you do? / give me ideas / show me examples / getting started / what data do you have? — the onboarding entry point for an agent that just connected and wants to know what is worth asking. Returns category-bucketed example questions (company financials, drugs & clinical trials, economics, real estate, prediction markets, weather, government & patents, science & academia, news) — each with the exact tool + argument shape that answers it, drawn from the live catalog of thousands of tools. Call with no arguments for the full spread, or pass `topic` (e.g. "finance", "pharma", "betting") to focus. Use this FIRST when you do not yet know what Pipeworx can do for you, or to learn how to call the meta-tools (ask_pipeworx, entity_profile, compare_entities, etc.).

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

## Remotes

- https://gateway.pipeworx.io/bindingdb/mcp (streamable-http, auth none, reachable true, uptime30d 0.96)

## Packages

_none_

## Tools (0)

_none observed_