Server Quality Checklist

Tool Scores

• foldseek_search_structureC
  2.4/5.0
  Behavior2/5

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

  With no annotations, the description should disclose behavioral traits. It mentions 'easy-search' but does not explain the computational cost, GPU usage, or what the tool does beyond a vague term.

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

  Conciseness3/5

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

  The description is very concise with one sentence, but it sacrifices necessary detail. It is not verbose but is underinformative.

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

  Completeness1/5

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

  Given the tool's complexity (10 parameters, no annotations, output schema), the description is severely incomplete. It fails to cover purpose relative to siblings, parameter meanings, or behavioral context.

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

  Parameters1/5

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

  Schema description coverage is 0%, yet the description adds no explanation for any of the 10 parameters. Parameters like evalue, sensitivity, and alignment_type are left completely unexplained.

  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 clearly states the verb 'Run' and the resource 'FoldSeek easy-search with a PDB/mmCIF structure query'. However, it does not explicitly distinguish from the sibling tool foldseek_search_sequence which uses a sequence query.

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

  Usage Guidelines2/5

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

  No guidance is provided on when to use this tool versus alternatives like foldseek_search_sequence or prerequisites such as needing a valid PDB file.

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

• foldseek_search_sequenceC
  2.5/5.0
  Behavior2/5

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

  The description is minimal and does not disclose behavioral traits beyond the basic action. No annotations are provided, so the description carries the full burden. There is no mention of prerequisites, side effects, auth needs, or performance considerations. A score of 2 indicates significant missing transparency.

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

  Conciseness3/5

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

  The description is a single short sentence, which is concise but lacks structure. It is not overly verbose, but it sacrifices completeness. A score of 3 reflects that it is adequately concise but not well-structured for an AI agent to parse efficiently.

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

  Completeness1/5

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

  Given the tool has 12 parameters, no schema descriptions, and no annotations, the description is severely incomplete. It does not explain what FoldSeek easy-search does, how the query is processed, what the return format is (despite having an output schema), or any other contextual information. This is inadequate for an AI agent to use effectively.

  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?

  With 0% schema description coverage, the description must add extensive parameter meaning. However, it only mentions 'FASTA query' (vaguely covering fasta_path/fasta_text) and 'configured ProstT5 model' (covering the model parameter). The other 10 parameters (evalue, threads, database, etc.) are completely undocumented. This is insufficient.

  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 the action (Run) and resource (FoldSeek easy-search) with a FASTA query and ProstT5 model. This is clear enough, but it does not differentiate from sibling tool foldseek_search_structure, which likely searches by structure instead of sequence. A 5 would require explicit differentiation.

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

  Usage Guidelines2/5

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

  No guidance on when to use this tool versus alternatives like foldseek_search_structure or foldseek_validate_environment. The agent is left to infer from the name. This is a significant gap.

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

• foldseek_download_databaseC
  2.6/5.0
  Behavior2/5

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

  With no annotations, the description must disclose behavioral traits. It only mentions 'download or prepare', lacking details on network requirements, destructive potential, or permission needs. This is insufficient for safe invocation.

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

  Conciseness4/5

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

  The description is a single sentence, which is concise. However, it under-delivers on informativeness; while there is no fluff, the brevity sacrifices necessary detail.

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

  Completeness2/5

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

  Given the tool has two parameters, no annotations, and an output schema (not described), the description is incomplete. It fails to cover parameter semantics, usage context, or behavioral traits, leaving significant gaps for an agent.

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

  Parameters1/5

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

  Schema description coverage is 0%, but the description provides no explanation of the 'database' string parameter or the 'confirm_large' boolean. The agent cannot infer what values are valid or how to use them.

  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 clearly states the verb 'download' or 'prepare' and the resource 'catalog-listed FoldSeek database', distinguishing it from sibling tools that list, search, or validate. However, 'prepare' is somewhat ambiguous, preventing a perfect score.

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

  Usage Guidelines2/5

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

  No guidance on when to use this tool versus alternatives (e.g., foldseek_list_databases). Description implies use for downloading but does not specify prerequisites or conditions.

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

• foldseek_validate_environmentA
  3.5/5.0
  Behavior2/5

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

  Without annotations, the description carries full burden for behavioral transparency, but only states 'validate' without describing side effects, authorization needs, or what happens on success/failure. No annotation contradiction.

  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 a single concise sentence, front-loaded with the verb, with no unnecessary words.

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

  Completeness3/5

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

  With no parameters and an output schema, the description is adequate but minimal. It does not explain what 'validate' checks or what the output indicates, though the output schema likely covers return values.

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

  Parameters4/5

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

  Input schema has 0 parameters, so schema coverage is 100%. The description adds context by mentioning 'local FoldSeek MCP runtime environment', which is a baseline 4 for zero parameters.

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

  Purpose5/5

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

  The description clearly states the tool validates the local FoldSeek MCP runtime environment, using a specific verb and resource. It distinguishes from sibling tools which handle searching, downloading, and listing.

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

  Usage Guidelines2/5

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

  The description provides no guidance on when to use this tool versus alternatives or prerequisites. It is implied to be a prerequisite but not explicitly stated.

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

• foldseek_list_databasesA
  4.2/5.0
  Behavior3/5

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

  No annotations are provided, so the description carries the full burden. 'List' implies a read-only operation, but the description does not disclose whether network calls are involved or any potential side effects.

  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 a single, efficient sentence with no wasted words. It front-loads the core action and resource.

  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 zero-parameter list tool, the description is adequate. An output schema exists, so return values are handled. Minor improvement could mention output format.

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

  Parameters4/5

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

  No parameters exist, so the description does not need to add parameter meaning. The schema coverage is 100%, meeting the baseline for zero parameters.

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

  Purpose5/5

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

  The description clearly states the tool lists installed and available FoldSeek databases and model resources, matching the name and distinguishing from sibling tools that perform downloads, searches, or validation.

  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 (listing resources) with no need for exclusions. It implicitly suggests using this before downloading or searching, though lacks explicit when-to-use guidance.

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