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maintenanceProvides a collection of MCP servers for computational chemistry tasks including molecular generation and retrosynthesis. Also offers property prediction and molecule pricing capabilities.
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"Search for Open Source Intelligence (OSINT) Tools" matching MCP servers:
- Flicense-qualityCmaintenanceEnables searching for academic papers and preprints across multiple platforms including Semantic Scholar, arXiv, PubMed, and CrossRef. It provides access to research records, DOI lookups, and journal metadata through a unified interface deployed on Cloudflare Workers.
- AlicenseBqualityDmaintenanceServer to search PubMed (PubMed is a free, online database that allows users to search for biomedical and life sciences literature). I have created on a day MCP came out but was on vacation, I saw someone post similar server in your DB, but figured to post mine.147MIT
- Flicense-qualityDmaintenanceEnables search and retrieval of academic papers from PubMed database with advanced features like MeSH term lookup, publication statistics, and PICO-based evidence search.5
- AlicenseAqualityDmaintenanceEnables AI-driven pharmacogenomic analysis by querying structured genetic variant, drug response, and disease risk data. Supports natural language questions about medications, traits, and health risks based on user genome data, with privacy-first local execution.1645511MIT
- Alicense-qualityDmaintenanceEnables deep probabilistic analysis of single-cell omics data using scvi-tools through natural language. Supports SCVI for scRNA-seq analysis, SCANVI for cell type annotation, TOTALVI for multi-modal RNA/protein data, and PEAKVI for scATAC-seq analysis.MIT
- Alicense-qualityDmaintenanceA specialized MCP server for Metal-Organic Framework research that provides tools for database searching, structural optimization, and energy calculations via ASE. It enables scientific workflows by allowing users to interact with MOF data and perform chemical simulations through a standard SSE interface.MIT
- Alicense-qualityCmaintenanceEnables searching cryo-EM density maps in EMDB and raw datasets in EMPIAR, with filtering by resolution, keyword, and cross-referencing between the two databases.MIT
- -license-quality-maintenanceThis server enables multi-agent conversations for interacting with Cirro's biological data platform through its OpenAPI interface, auto-generated using AG2's MCP builder.
peptoma-mcpofficial
Alicense-qualityDmaintenanceAn MCP server that connects AI agents to the PEPTOMA open DeSci peptide research platform, enabling peptide sequence analysis, feed search, and peer-review annotations.25MIT- Alicense-qualityAmaintenanceBioMCP is an open-source MCP server that connects any AI assistant to 15 open bioinformatics databases with zero configuration. It provides 23 tools for literature, sequences, BLAST, structures, enrichment, annotations, genomes, interactions, variants, domains, compounds, and single-cell data.1MIT
- Alicense-qualityAmaintenanceResolve one supported GRCh38 germline variant and return structured, source-backed ACMG/AMP evidence with provenance and explicit limitations. The public server is read-only and intended for professional review.Apache 2.0
- Alicense-qualityCmaintenanceEnables querying metadata from MyVariant.info, a comprehensive variant annotation database, providing dataset statistics, source information, and build versions.7MIT
Ask Helenaofficial
Flicense-qualityCmaintenanceOfficial public, read-only Helena Bioinformatics MCP for source-cited answers about the company and its published products.- Alicense-qualityCmaintenanceEnables AI agents to query the WikiPathways open community pathway database via natural language, part of the Pipeworx MCP gateway.3MIT
- Alicense-qualityBmaintenanceReproduces the in-silico toxicological profile of Heracleum sosnowskyi metabolites from Rassabina & Fedorov (2025) using open-source models for LD50 prediction, toxicity classification, chemical space clustering, and synthesis cost estimation.MIT
- Flicense-qualityDmaintenanceEnables LLMs and AI agents to query a biomedical knowledge graph stored in RedisGraph, with tools for concept search, synonym enrichment, and study variable discovery through semantic relationships.
- AlicenseAqualityAmaintenanceAn MCP server that grounds protein research in the UniProt SPARQL endpoint, providing tools for querying proteins, sequences, variants, diseases, and more via intent-named tools and raw SPARQL.15MIT
- AlicenseAqualityBmaintenanceEmpowers AI agents with direct access to the official ClinicalTrials.gov database, enabling programmatic searching, retrieval, and analysis of clinical study data through a Model Context Protocol interface.71,14987Apache 2.0
- AlicenseAqualityAmaintenanceMCP server and Claude Plugin for a full ENCODE Project genomic data and analysis toolkit — search, download, track, and analyze functional genomics experiments208526AGPL 3.0
