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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.
74,293 servers. Updated
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"Coding tools to understand and manage a large codebase like MCP, CLINE, or ROOCODE" matching MCP servers:
- 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
- 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-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
- FlicenseAqualityDmaintenanceEnables AI assistants to clean PDB structures and run initial-stage energy relaxation for biomolecular modeling. It provides a structured workflow for preparing structures before production molecular dynamics or coarse-graining pipelines.9
- AlicenseAqualityCmaintenanceEnables coding agents to interact with the Reactome pathway database, including search, lookup, hierarchy traversal, SBML/SBGN export, and gene-set enrichment analysis.17MIT
- AlicenseAqualityAmaintenanceA bridge connecting AI agents to NCBI's PubMed database through the Model Context Protocol, enabling seamless searching, retrieval, and analysis of biomedical literature and data.113,327134Apache 2.0
- AlicenseAqualityAmaintenancePhylogenetic inference server driving IQ-TREE 2, always returning per-clade bootstrap support plus model selection, tree comparison, and alignment simulation, with detailed diagnostics like conflicting clades and model uncertainty.5GPL 2.0
- AlicenseAqualityDmaintenanceA Model Context Protocol server that interfaces with Biomart databases, allowing models to discover biological datasets, explore attributes/filters, retrieve biological data, and translate between different biological identifiers.88MIT
- AlicenseAqualityBmaintenanceMCP server that exposes the UniProt REST API to LLM clients, enabling search and retrieval of protein data via tools like search_uniprotkb, get_entry, and map_ids.7MIT
- AlicenseAqualityFmaintenanceAn MCP server that enables AI coding assistants to interact with Rosetta, PyRosetta, and Biotite for running RosettaScripts, validating XML, translating between Rosetta and Biotite, scoring structures, and querying documentation.1911218MIT
- AlicenseAqualityAmaintenanceIntegrates AlphaFold DB and eight other biomedical data sources into MCP tools for variant clinical reporting, disease-target analysis, structural intelligence, and drug repurposing, with results persisted to a local SQLite knowledge graph.304Apache 2.0
- AlicenseAqualityCmaintenanceAn MCP server that provides standardized access to biomedical knowledge bases and resources, enabling AI systems to retrieve verified information from sources like bioRxiv, EuropePMC, and various protein/gene databases.5228Apache 2.0
- AlicenseAqualityDmaintenanceEnables AI assistants to query the Ubergraph biomedical ontology SPARQL endpoint with tools for custom SPARQL queries, term lookup, search, and hierarchy traversal.4MIT
- AlicenseAqualityDmaintenanceProvides an MCP interface to the ROBOT command-line tool for OWL ontology editing, enabling operations like merging, reasoning, and conversion via natural language.261BSD 2-Clause "Simplified"
- AlicenseAqualityDmaintenanceEnables AI agents to conversationally interact with genomics research networks for data analysis and discovery across multiple Omics AI Explorer platforms. It provides tools for exploring data collections, examining table schemas, and executing SQL queries against datasets like Viral AI and Neuroscience AI.61MIT
- FlicenseAqualityDmaintenanceLeverages large language models to analyze users' WeGene genetic testing reports, providing access to report data via custom URI schemes and enabling profile and report management through OAuth authentication and API utilization.44
- FlicenseBqualityDmaintenanceA comprehensive Model Context Protocol (MCP) server for accessing the STRING protein interaction database. This server provides powerful tools for protein network analysis, functional enrichment, and comparative genomics through the STRING API.64
