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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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"Using a Browser with Dev Tools to Debug a Web Application" matching MCP servers:
- AlicenseAqualityCmaintenanceEnables genomic sequence analysis through the Evo 2 model, supporting DNA sequence scoring, embedding, generation, and variant effect prediction with multiple model checkpoints (7B, 40B, 1B parameters).62LGPL 3.0
- AlicenseAqualityCmaintenanceEnables variant annotation and effect prediction using the Ensembl VEP API, with support for batch and single queries.91MIT
- 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
- AlicenseBqualityDmaintenanceProvides comprehensive access to the UCSC Genome Browser API, enabling queries of genomic data, DNA sequences, gene annotations, variants, and metadata across multiple species and assemblies.126MIT
- 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-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
- FlicenseAqualityCmaintenanceEnables analysis of bulk RNA-seq data using natural language queries, executing R and Python in a Docker container with automatic sample anonymization and privacy controls.7
- FlicenseBqualityFmaintenanceA comprehensive Model Context Protocol server providing access to over 110 million chemical compounds with extensive molecular properties, bioassay data, and chemical informatics tools from the PubChem database.3046
Cytoscape MCP Serverofficial
Alicense-qualityAmaintenanceAn embedded MCP server for Cytoscape Desktop that lets AI agents load networks, set active views, and control the desktop application over HTTP.6BSD 3-Clause- Alicense-qualityBmaintenanceExposes pipen bioinformatics pipelines as MCP tools, allowing AI assistants to discover and run complex workflows through a progressive disclosure interface.1MIT
- Alicense-qualityDmaintenanceAn MCP server for running local LLMs using llama-cpp-python, with built-in tools for generating drug-like molecule SMILES.3MIT
- Alicense-qualityCmaintenanceEnables querying the Human Protein Atlas data using natural language or direct MCP tools, with keyless access via the Pipeworx gateway.5MIT
- Alicense-qualityFmaintenanceA Model Context Protocol server that enables AI assistants to interact with LAMMPS for molecular dynamics simulations through natural language commands.14Apache 2.0
- Alicense-qualityCmaintenanceMCP server for biological protein design, folding, and affinity prediction using Refua tools, with optional support for ADMET, clinical simulation, preclinical planning, wet-lab automation, and more.MIT
- Flicense-qualityCmaintenanceProvides a natural language interface for single-cell RNA-Seq analysis using the decoupleR framework. It enables users to perform biological pathway inference, data clustering, and visualization through MCP-compatible AI clients.4
- Flicense-qualityCmaintenanceA self-driving cheminformatics MCP server that dynamically exposes a growing library of RDKit-based molecular analysis tools (fingerprints, descriptors, substructure matching, drug-likeness filters, and more) as MCP tools, with each skill autonomously implemented and tested by an agent loop without human intervention.
- 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.
- Flicense-qualityCmaintenanceProvides a natural language interface for inferring Copy Number Variations (CNVs) from scRNA-Seq data using the infercnvpy framework. It enables users to perform data preprocessing, CNV inference, and visualization through chromosome heatmaps, UMAP, and t-SNE plots.2
- Flicense-qualityDmaintenanceA Model Control Protocol implementation for SAMtools, providing a standardized interface for working with SAM/BAM/CRAM files.