"How to find or generate YouTube video transcripts" matching MCP servers:

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.

A 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.

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.

Enables users to generate volcano plots by submitting jobs with input files and parameters, supporting local or Docker execution.

Enables querying of per-residue missense tolerance, Pfam domain annotations, and variant counts for human transcripts by wrapping the MetaDome web service. Provides MCP tools for resolving transcripts, requesting tolerance landscapes, and identifying constrained regions.

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

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 AI assistants to generate publication-quality bioinformatics visualizations (volcano plots, PCA, heatmaps, etc.) directly from raw biological data.

Searches UniProt by protein name to find accession numbers and retrieves detailed protein structure information from AlphaFold, including direct links to 3D structural predictions.

MCP server for RNA-seq downstream analysis, wrapping R scripts to generate plots and perform analyses like PCA, volcano, heatmap, enrichment, and WGCNA.

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 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 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.

A Model Context Protocol (MCP) server for interacting with Gen3 data commons, with GraphQL query validation to reduce hallucinations.

Provides read-only access to the ProPaths verified protein interactome, letting AI agents search proteins, retrieve mechanistic interaction details, and explore pathway ontology through MCP tools, resources, and prompts.

A 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.

An MCP server that provides mouse genetics data from Mouse Genome Informatics (MGI), enabling LLM agents to query markers, mutations, alleles, phenotypes, and disease models.

MCP 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.

Enables AI assistants to run reproducible bioinformatics pipelines over MCP, with verifiable provenance via checksums and Workflow Run RO-Crate metadata.

An 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.

Enables MCP clients to annotate and classify single human genetic variants in any notation, returning an auditable points-based ACMG verdict with its criteria, gnomAD frequencies, in-silico predictors, ClinVar data, and per-transcript consequences. It is read-only, requires no account or API key, and keeps answers compact while linking back to the source.

Enables AI assistants to rapidly gather and synthesize structural, chemical, conservation, and literature data about protein binding pockets for drug-target triage. Useful as a reconnaissance step before computational binder design.

Empowers AI agents with direct access to the official ClinicalTrials.gov database, enabling programmatic searching, retrieval, and analysis of clinical study data through a Model Context Protocol interface.

MCP server for polygenic risk score analysis, wrapping just-prs to enable catalog search, PRS computation, VCF normalization, percentile and risk estimation, and quality assessment.