protein-tools-mcp

Overview Schema Source Related Servers Discussions Admin

validate_pdb

Validate PDB or mmCIF files for downstream MD, docking, or analysis. Reports format errors, non-standard residues, altLocs, chain gaps, and other issues to catch before pipeline use.

Instructions

Validate a PDB or mmCIF structure file (AlphaFold 3 / RCSB) for downstream use (MD prep, docking, analysis).

Reports atom/residue/chain counts, fixed-column format errors, non-standard residues, altLocs, chain gaps, duplicate atom names, insertion-code residues, and multi-model (NMR) notes. Always run this before feeding a structure into a pipeline.

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": "validate_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

A3.9/5.0

Behavior4/5

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

With no annotations provided, the description carries the full behavioral burden. It substantively discloses what the tool checks and reports—format errors, non-standard residues, altLocs, chain gaps, duplicate atom names, insertion-code residues, and multi-model notes—which is rich behavioral context. It does not explicitly state side effects or error-handling behavior, but for a validation tool the enumerated checks provide strong transparency.

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?

The description is front-loaded with the core purpose, followed by a well-structured list of checks, and ends with a clear usage directive. Every sentence earns its place, and there is no wasted verbiage.

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

Completeness5/5

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

An output schema exists, so the description need not explain return values. Given the low complexity (one parameter, no annotations), the description covers purpose, what is validated, and when to use it, making it complete enough for an agent to invoke correctly.

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 coverage is 0%, and the single parameter 'pdb_path' has no schema description. The description only implies the input is a PDB or mmCIF file, adding minimal meaning beyond the parameter name and schema title. It does not explain path format, file existence requirements, or other practical semantics.

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?

The description states a specific verb and resource: 'Validate a PDB or mmCIF structure file (AlphaFold 3 / RCSB) for downstream use.' It enumerates the validation checks it performs, which helps distinguish it from sibling tools like structure_stats, but it does not explicitly name an alternative sibling, keeping it at a 4 rather than 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 Guidelines4/5

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

The description provides clear context for when to use the tool: 'Always run this before feeding a structure into a pipeline.' However, it does not name any alternative tools or specify when NOT to use it, so it falls short of the 5-level criteria for explicit when/when-not/alternatives.

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