"Retrieving information from document directory with search and memory capabilities" matching MCP servers:

Enables 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.

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 search and retrieval of academic papers from PubMed database with advanced features like MeSH term lookup, publication statistics, and PICO-based evidence search.

An MCP server for searching and accessing RNA sequencing datasets from the European Nucleotide Archive (ENA), supporting bulk, single-cell, and spatial transcriptomics with advanced filtering and download capabilities.

An 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.

Provides seamless access to the Protein Data Bank in Europe (PDBe) API and search capabilities, enabling AI clients to query protein structures, perform advanced searches, and retrieve structural biology data.

Enables searching, retrieving, and downloading protein structure data from the RCSB Protein Data Bank. Supports intelligent protein structure search, comprehensive data retrieval, and multiple file format downloads for bioinformatics research.

Enables AI assistants to access protein information directly from UniProt, allowing retrieval of protein names, functions, sequences, and organism data by accession number.

Allows to retrieve information about an AnnData object via MCP using the read_lazy function from anndata.

Enables AI assistants to query genetic variant data, gene constraints, and population genetics information from the gnomAD (Genome Aggregation Database) through its GraphQL API. Supports searching for genes and variants, retrieving constraint scores, analyzing population frequencies, and accessing genomic coverage data.

A Model Context Protocol server that enhances language models with protein structure analysis capabilities, enabling detailed active site analysis and disease-related protein searches through established protein databases.

A server that enables AI assistants to interact with cancer genomics data from cBioPortal, allowing users to explore cancer studies, access genomic data, and retrieve mutations and clinical information.

Enables AI agents to search, filter, download files, and generate reports from the IGVF Data Portal using natural language commands.

Enables querying the gnomAD genome aggregation database for variant, gene, and region information.

MCP-native scientific skills for reproducible computational biology and AI-driven drug-discovery workflows. It combines deterministic scientific tools with an MCP server to give AI agents real computational capabilities.

Enables querying and browsing ontologies from the EBI Ontology Lookup Service, including searching for terms, retrieving term details, and navigating ontology hierarchies via natural language.

Enables querying and retrieving bacterial and viral genomic data, features, antimicrobial resistance, and epitopes from the BV-BRC API using natural language.

A Model Context Protocol server providing programmatic access to 3D protein structural data from RCSB PDB, PDBe, and UniProt, enabling search, retrieval, comparison, and analysis of protein structures.

Enables querying metadata from MyVariant.info, a comprehensive variant annotation database, providing dataset statistics, source information, and build versions.

Provides tools to query and resolve identifiers from the Bioregistry, including prefix metadata, CURIE resolution, and substring search.