"Enhanced MCP-Reasoner with Monte Carlo Tree Search and Beam Search Integration" 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.

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

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 AI agents to resolve scientific (Latin binomial) names to Open Tree of Life taxon IDs, retrieve full taxonomic details, synonyms, and ancestor lineages, and find the most recent common ancestor of up to 10 taxa within the synthetic tree of life. Runs keylessly over a hosted gateway endpoint or locally via npx.

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

Phylogenetic 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.

Enables LLM agents to search biomedical literature, retrieve article details, find related papers, manage caching, and download open-access full texts through MCP with structured, agent-friendly responses.

Biological and medical data search MCP server.

Enables AI assistants to query the Ubergraph biomedical ontology SPARQL endpoint with tools for custom SPARQL queries, term lookup, search, and hierarchy traversal.

Enables LLM-powered applications to look up bacterial and archaeal taxonomy, search genomes, browse and navigate the taxonomic tree, and compare genomes or find phylogenetic paths between taxa. It works out of the box with a built-in reference dataset covering major phyla and can be pointed at full Genome Taxonomy Database TSV files for comprehensive queries.

Search PubMed for articles matching the query.

Enables integration between MCP-compatible clients and APIs registered in the SmartAPI registry, allowing seamless discovery and interaction with bioinformatics and life sciences APIs through standardized MCP protocols.

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 agents to search public cancer genomics studies (TCGA, CPTAC, MSK, and more), fetch full details for individual studies, resolve gene symbols to Entrez ids, and list cancer types. Works keylessly against open cBioPortal data over a hosted MCP endpoint, a local stdio server, or plain HTTP.

Enables AI agents to search and retrieve compounds, drugs, diseases, pathways, genes, enzymes, glycans, modules, and KO entries; fetch full parsed flat-file entries by ID; and list database contents through keyless REST tools.

Provides access to BioThings.io APIs for comprehensive gene and variant annotations, enabling seamless integration of biological data into workflows.

Enables agents to search protein family, domain, and functional-site entries, read entry metadata and clan relationships, map a UniProt protein's annotations to residue coordinates, and find proteins carrying a given signature. Runs over STDIO or Streamable HTTP with no credentials required.

Enables life-science research by providing search and retrieval across linked publications, clinical trials, drugs, genes, regulatory approvals, and patents through MCP clients.

Enables AI assistants to automate iTOL phylogenetic tree visualization workflows, including tree inspection, taxonomy and monophyly analysis, annotation template generation, batch uploads, and export through 33 tools, 3 resources, and 2 prompts.

🔍 Enable AI assistants to search, access, and analyze PubMed articles through a simple MCP interface.

Federates 13 gene-related MCP backends (gnomAD, GTEx, etc.) behind a single Streamable HTTP endpoint with collision-free namespacing and search-based tool discovery.

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 search and access to MGnify public microbiome studies, biome vocabulary, and ~57,000 MAGs and isolate genomes with completeness, contamination, and GTDB taxonomy.

Enables users to look up yeast genes/loci, search genes and alleles by free text, and retrieve Gene Ontology annotations from the Saccharomyces Genome Database.

Enables term search, class lookup, and cross-ontology mappings across NCBO BioPortal's ~1,300 biomedical ontologies.

Enables AI assistants to query VirtualFlyBrain data, run queries, and search for terms related to Drosophila neurobiology.

Provides access to UniProt protein sequence and function knowledge base, enabling search and retrieval of protein entries, proteomes, taxonomy, and feature annotations.

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

MCP server for Addgene plasmid repository, enabling AI assistants to search, filter, and retrieve plasmid data including sequences and metadata.

MCP server for Ketcher chemical structure editor integration, enabling SMILES/MOL/InChI conversion, image generation, molecular property calculation, and validation.