"Using Cherry Studio Tool on Windows to Connect to MySQL MCP Server" matching MCP servers:

Provides an MCP interface to the ROBOT command-line tool for OWL ontology editing, enabling operations like merging, reasoning, and conversion via natural language.

Provides access to EMBL-EBI bioinformatics data including InterPro domains, Pfam families, protein features, and taxonomy through a unified tool.

MCP server that exposes DECIMER image-to-SMILES functionality as tool calls.

Server 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.

Enables MCP clients and the cheminfo chat to call one catalog of tools while carrying produced structures, reaction schemes, spectra and files beside the answer rather than through the model. It provides tool listing, tool invocation, and stateless Streamable HTTP MCP endpoints.

Enables AI assistants to perform quality control analysis on high-throughput sequencing data using FastQC and MultiQC. It supports single-file and batch processing of FASTQ/FASTA files and generates comprehensive, interactive summary reports.

MCP server for interacting with Galaxy bioinformatics platform, enabling AI assistants to connect to Galaxy instances, search and execute tools, manage workflows, and access other features.

Enables AI clients to connect to Galaxy instances, inspect histories and reports, discover tools and workflows, submit analyses, and monitor their results via interactive cards.

Enables querying roughly 3.2 million measured protein–ligand binding affinities from a local, read-only DuckDB build of the BindingDB MySQL dump, with tools for searching compounds and targets, retrieving potency and selectivity profiles, fetching activity records with assay and citation details, and running read-only SQL.

This server provides access to InterPro protein family, domain, and functional-site classification data from EBI. It allows querying protein annotations through natural language or direct tool calls.

Validates the physical and chemical plausibility of ligand–protein docking poses using the PoseBusters tool.

Enables language models to search biomedical literature, fetch sequences, and follow links across Entrez databases through eleven read-only tools wrapping the nine NCBI Entrez E-utilities. It handles URL building, pacing, redirects, response caps, and API-key redaction so queries can be answered without a browser or scraping.

Grounds gene-nomenclature work in the HUGO Gene Nomenclature Committee (HGNC) dataset, enabling resolution of gene symbols and IDs to canonical HGNC identifiers, plus cross-references and batch operations.

Enables 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.

MCP server that provides tools to query harmonized gene-disease validity data from the Gene Curation Coalition, supporting consensus and conflict detection for gene-disease assertions.

Enables DNA sequence analysis and variant effect prediction using Evo2-7B via MCP tools, providing forward inference, likelihood scoring, and batch variant comparison through natural language.

Enables AI agents to retrieve cited pharmacogenomic and gene-variant information, including drug–gene guidance from CPIC/DPWG and rsID lookups, so responses can quote curated sources instead of relying on memory. A local package also lets users read raw DNA files on their own computer without sending the file data to the remote service.

Enables coding agents to interact with the Reactome pathway database, including search, lookup, hierarchy traversal, SBML/SBGN export, and gene-set enrichment analysis.

Provides direct SQL access to a locally hosted Reactome database, enabling schema discovery, guarded read-only queries, and ergonomic helpers over the full relational schema.

Guides researchers, including those new to BPP, from raw sequence data to a validated control file that has passed a short test run. Wraps BPP command-line tools without running long analyses itself.