protein-tools-mcp

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sequence_from_pdb

Extract one-letter amino-acid sequences per chain from a PDB file, handling MD protonation variants and using model 1 for multi-model files.

Instructions

Extract one-letter amino-acid sequences per chain from a PDB file (handles MD protonation variants; for multi-model files uses model 1).

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "pdb_path": "<pdb_path>"
    },
    "name": "sequence_from_pdb"
  }
}

Input Schema

Name	Required	Description	Default
`pdb_path`	Yes

Output Schema

Name	Required	Description	Default
`result`	Yes

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.0Oct 20, 2026

TDQS

A3.6/5.0

Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With no annotations, the description carries the full behavioral burden and does disclose non-obvious traits: it handles MD protonation variants and selects model 1 for multi-model files. That is meaningful edge-case context an agent could not infer. It omits any note on output shape, though an output schema exists to cover that.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

A single front-loaded sentence with zero filler; the parenthetical edge-case handling is compact and earns its place rather than padding the definition.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

For a one-parameter extraction tool with an output schema covering return values, the description is nearly complete—purpose plus edge-case behavior. The main residual gap is parameter-level detail, but nothing critical for calling the tool is missing.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters2/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 0%, so the description must compensate for the single undocumented pdb_path parameter. It only indirectly implies a PDB file is the input, adding no format, path, or validity detail beyond that, leaving the parameter largely unspecified.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

States a specific verb and resource: 'Extract one-letter amino-acid sequences per chain from a PDB file.' An agent can immediately tell what it produces. It does not explicitly contrast itself with nearby siblings like aa_composition, read_fasta, or detect_sequence_type, so it stops short of a 5.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The scope ('per chain', 'from a PDB file') implies when it applies, but there is no explicit when-to-use or when-not-to-use guidance and no alternative named among the many sequence/FASTA siblings. Usage is inferable but not stated.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.