Bindingdb
NPM · @PIPEWORX/MCP-BINDINGDB · 2 COMPONENTS
BindingDB — measured protein/small-molecule binding affinities.
Available components
Last scanned (7 hours ago)
Scores higher than 76% of npm servers
Category Health and Science
How this component scores in each security and reliability category. Every signal is checked automatically from public evidence about the published package, including repeated runs of it in an isolated sandbox, and we only credit what we can confirm. How we score → Why this is hard to score →
Supply Chain Security100
- No malware found by supply-chain analysis.Pass
- No known CVEs affecting this package version or its production dependencies.Pass
- No install/post-install scripts declared.Pass
- No production dependencies, so there is no dependency health to assess. View diagnostics → Pass
Provenance & Transparency97
- Source repository is publicly reachable at the declared URL. View diagnostics → Pass
- Cryptographically verified build provenance (signed, bound to pipeworx-io/mcp-bindingdb). View diagnostics → Pass
- Clear OSI-approved license (MIT).Pass
- Actively maintained (last published 5 days ago).Pass
- Disclosure check failed: no security disclosure policy was found in the source repository. See how to fix → Fail
Schema Quality & AI Usability68
- AI-judged instruction clarity (good).Pass
- Context-footprint check failed: tool/resource definitions use about 559 tokens (~186/item across 3 items; 3 tools + 0 resources), over budget; trim descriptions and params. See how to fix → Fail
- Usage-examples check failed: none of the tools include examples. See how to fix → Fail
Stability & Change Management23
- Stability observed for 7 of 30 days with no destabilising changes; credit accrues until the full window elapses.Partial
Tool Coverage100
- 100% of tools have a non-trivial description (not blank, and not just the tool's name).Pass
- 100% of tool parameters carry a description.Pass
Tool Safety100
- No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.Pass
- We read all 3 captured tool definition(s), and no name or description among them implies an irreversible operation.Pass
- An AI judge read all 4 captured unit(s) of tool text and found none that tries to manipulate the model reading it.Pass
Capabilities100
- Implements a supported MCP spec version (2025-11-25); the latest is 2026-07-28.Pass
Every change we have recorded for this component, newest first. Security-relevant changes are always shown. ▲ marks a change for the better, ▼ a change for the worse; unmarked changes are neutral.
- 5 Nov 26 +1
No change was recorded against any check on this day. Stability & Change Management went from 20 to 23. That category is still filling its 30-day observation window: 6 days of observed history at the previous scan, 7 at this one. The score rises as the window fills, whether or not the server changes.
- 3 Nov 26 +1
No change was recorded against any check on this day. Stability & Change Management went from 13 to 17. That category is still filling its 30-day observation window: 4 days of observed history at the previous scan, 5 at this one. The score rises as the window fills, whether or not the server changes.
- 31 Oct 26 +16
- Malware scan: unverified → pass ▲ security
- 30 Oct 26 −15
- Malware scan: pass → unverified ▼ security
- Package version: 0.2.0 → 0.2.1 functional
- 29 Oct 26 80
First indexed and scored.
Diagnostic detail from the automated scan of this channel: what the scanner observed at each step, so you can see exactly where a check passed or failed. It is informational only and never changes the trust score.
Captured 5 Nov 2026 · Analysed npm/@pipeworx/mcp-bindingdb@0.2.1
Provenance Verified
A signed build attestation was found and verified, binding this exact artifact to the source repository it claims to come from.
| Result | Verified |
|---|---|
| Ecosystem | npm |
| Reason | Verified |
| Discovered via | Registry attestation endpoint |
| Source repo | pipeworx-io/mcp-bindingdb |
| Certificate issuer | https://token.actions.githubusercontent.com |
| Certificate SAN | https://github.com/pipeworx-io/mcp-bindingdb/.github/workflows/publish.yml@refs/heads/main |
| Rekor log index | 3601440084 |
| Predicate type | SLSA build provenance https://slsa.dev/provenance/v1 |
| Subject digest | sha512:db230459a26a14f7df919c39dae4157bbd345844799cd7c3e38109d03a609b41587e5fd1914c7ea996cb37931ba9f1bfe902dbd5d3ae83b458e23ab6f |
Background: How many MCP packages publish verified provenance →
Dependencies 0 packages
| Packages resolved | 0 |
|---|---|
| Tree resolution | Complete |
Background: SBOMs and build attestations, explained →
The tools this component advertises to a client, with an estimated token cost for each. Expand a tool to see its parameters and schema. The per-tool counts are indicative and are not scored directly; the schema's total context footprint is one signal in Schema Quality & AI Usability. A tool's description is untrusted text the model reads on every call, which is what makes this list a security surface and not just an inventory: how tool poisoning works →
bindingdb_by_pdb ~123
Measured binding affinities for the ligands associated with a PDB structure entry, linking a solved co-crystal to the potency numbers published for that target. AUTHORITATIVE for "what is the measured affinity of the ligand in this PDB structure". Takes a single 4-character PDB ID (e.g. 3EML).
| Name | Type | Req | Description |
|---|---|---|---|
| limit | number | – | Max rows to return, 1-500 (default 50) |
| pdb | string | yes | PDB entry ID, 4 characters (e.g. "3EML") |
No output schema declared.
No examples provided.
bindingdb_ligands_by_uniprot ~221
Measured binding affinities (Ki, Kd, IC50, EC50 in nM) for every ligand BindingDB has curated against a UniProt target, each with the PubMed ID of the paper it was measured in. AUTHORITATIVE for "what compounds bind this protein and how tightly" — this is experimental medicinal-chemistry data, not a prediction or a web summary. Pass one or more UniProt accessions (e.g. P24941 for CDK2).
| Name | Type | Req | Description |
|---|---|---|---|
| cutoff | number | – | Affinity cutoff in nM — only measurements at or below this are returned. Default 10. Raising it enlarges the upstream response substantially (100 nM on a well-studied kinase is several MB). |
| limit | number | – | Max rows to return, 1-500 (default 50). Sorted by potency. |
| uniprot | string | yes | UniProt accession, or several comma-separated (e.g. "P24941" or "P24941,P00533") |
No output schema declared.
No examples provided.
bindingdb_targets_by_smiles ~163
Given a compound SMILES, the protein targets BindingDB has measured it (or a structurally similar compound) against, with species and affinity. AUTHORITATIVE for compound-to-target and off-target lookups grounded in published measurements. Use a similarity cutoff below 1.0 to pull analogues as well as the exact structure.
| Name | Type | Req | Description |
|---|---|---|---|
| limit | number | – | Max rows to return, 1-500 (default 50) |
| similarity | number | – | Tanimoto similarity cutoff 0-1 (default 0.85). 1.0 means exact structure only. |
| smiles | string | yes | Compound SMILES (e.g. "CC(=O)Oc1ccccc1C(=O)O" for aspirin) |
No output schema declared.
No examples provided.
How do I install the Bindingdb MCP server?
Bindingdb runs locally as an npm package, launched with npx -y @pipeworx/mcp-bindingdb. Ready-made configuration for Claude, Cursor, VS Code, Codex and 5 more is on this page, copied from each client's own documentation.
npm · @pipeworx/mcp-bindingdb
claude mcp add pipeworx-io-bindingdb -- npx -y @pipeworx/mcp-bindingdb
What is the Bindingdb MCP server?
Bindingdb is an MCP server listed in the public MCP registry as io.github.pipeworx-io/bindingdb. BindingDB, measured protein/small-molecule binding affinities. This page covers its npm package (@pipeworx/mcp-bindingdb).
Is the Bindingdb MCP server safe to use?
Bindingdb scores 83 out of 100 on VerifyMCP. We found no known CVEs affecting it as of 5 November 2026. It declares no install or post-install scripts. Its build provenance is signed and verified. That is a record of what we were able to check automatically, not an endorsement. The category breakdown on this page shows every signal behind the number, including the ones we could not confirm.
What tools does the Bindingdb MCP server expose?
Bindingdb exposes 3 tools: bindingdb_ligands_by_uniprot, bindingdb_targets_by_smiles, bindingdb_by_pdb. Their descriptions and schemas cost roughly 507 tokens of context every time the server is loaded.
Is the Bindingdb MCP server still maintained?
Bindingdb is still listed as active in the MCP registry. We last reached this channel on 5 November 2026. Those dates come from our own scans of the registry and the channel itself, not from anything the publisher announced.
What licence is the Bindingdb MCP server under?
Bindingdb declares the MIT licence, which is OSI-approved. That covers the source only, and says nothing about the cost of any service it calls.