{"id":"dogeplusplus-bio-agents-mcp","name":"bio-agents-mcp","homepage":null,"repo_url":"https://github.com/dogeplusplus/bio-agents-mcp","category":"ai-ml","subcategories":[],"tags":["mcp","fastmcp","agents","bioinformatics","protein-data-bank","chembl","llm","chainlit","ollama","python","microservices"],"what_it_does":"bio-agents-mcp is a set of FastMCP-based microservices and a client for natural-language interaction with life-science data sources, specifically providing MCP servers for the Protein Data Bank (PDB) and (as described) ChEMBL, plus an LLM client and a Chainlit web UI for local use/testing.","use_cases":["Ask questions about protein/structure information from PDB through an MCP tool interface","Retrieve related annotations described in the module list (e.g., UniProt annotations, PubMed annotations, structural/assembly/cluster data)","Build an agent workflow that uses MCP tools for life-science data retrieval","Local experimentation with an MCP-based architecture using a local LLM (Ollama)","Integrate life-science data querying into an LLM app via a provided client"],"not_for":["Production deployments that require strong, documented security controls and enterprise-grade compliance (not evidenced in provided README)","Use cases needing a documented, stable public API contract (OpenAPI spec, typed schemas, etc.)","Scenarios requiring guaranteed uptime or formal SLAs (not evidenced)","Environments where outbound calls to external biological databases/APIs are disallowed"],"best_when":"You want local or controlled environment experimentation/agent prototyping around PDB (and ChEMBL per the description) using FastMCP and can review module READMEs/config for operational details.","avoid_when":"You cannot or will not run Docker Compose locally, or you require clearly specified auth/rate-limit/error-contract details from a single top-level API spec.","alternatives":["Official API clients/wrappers for PDB and ChEMBL","General purpose MCP client frameworks (FastMCP examples) with custom tool implementations","Workflow tools that call PDB/ChEMBL REST endpoints directly from your agent without MCP (custom REST tooling)"],"af_score":30.0,"security_score":39.0,"reliability_score":20.0,"package_type":"mcp_server","discovery_source":["github"],"priority":"low","status":"evaluated","version_evaluated":null,"last_evaluated":"2026-04-04T19:33:24.579932+00:00","interface":{"has_rest_api":false,"has_graphql":false,"has_grpc":false,"has_mcp_server":true,"mcp_server_url":null,"has_sdk":false,"sdk_languages":[],"openapi_spec_url":null,"webhooks":false},"auth":{"methods":[],"oauth":false,"scopes":false,"notes":"No authentication mechanism is described in the provided top-level README for the MCP servers or the client. The repository appears configured via .env, but auth specifics are not stated here."},"pricing":{"model":null,"free_tier_exists":false,"free_tier_limits":null,"paid_tiers":[],"requires_credit_card":false,"estimated_workload_costs":null,"notes":"No pricing information is applicable (open-source style repository; license is not specified in the provided metadata)."},"requirements":{"requires_signup":false,"requires_credit_card":false,"domain_verification":false,"data_residency":[],"compliance":[],"min_contract":null},"agent_readiness":{"af_score":30.0,"security_score":39.0,"reliability_score":20.0,"mcp_server_quality":55.0,"documentation_accuracy":35.0,"error_message_quality":0.0,"error_message_notes":null,"auth_complexity":40.0,"rate_limit_clarity":0.0,"tls_enforcement":60.0,"auth_strength":20.0,"scope_granularity":20.0,"dependency_hygiene":40.0,"secret_handling":60.0,"security_notes":"TLS/auth details are not specified in the provided README. Docker/local configuration suggests environment variables (.env), which is a positive sign for secret handling, but there is no explicit guarantee about logging/sanitization. As an MCP tool proxy to external biological data, it may expose sensitive query context if deployed without transport/auth controls.","uptime_documented":0.0,"version_stability":30.0,"breaking_changes_history":30.0,"error_recovery":20.0,"idempotency_support":"false","idempotency_notes":null,"pagination_style":"none","retry_guidance_documented":false,"known_agent_gotchas":["README does not document MCP tool schemas/arguments, pagination behavior, or retry/idempotency expectations; agents may need to handle API/transport limitations themselves.","Top-level README lists many functional items for the PDB module but does not show the actual tool names or response schemas; agents may require consulting module-level READMEs/config.","Authentication/rate-limit/error-contract details are not provided at the top level, which can lead to fragile agent behavior unless verified in module docs."]}}