"Top 100 MCP Servers Ranked by Weekly Downloads" matching MCP servers:

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 building and analyzing signalling networks from interaction databases through a Model Context Protocol server.

MCP server offering verified bioinformatics tools for sequence utilities and statistics, backed by BioPython/scipy. Enables AI agents to perform accurate GC content, translation, ORF finding, motif scanning, and statistical tests through natural language.

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 protein structure and sequence searches using FoldSeek, with support for multiple databases, automatic model downloads, and structured job management.

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

Enables AI assistants to perform NCBI BLAST sequence similarity searches through natural language, supporting nucleotide and protein searches, custom database creation, and multiple output formats.

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.

An MCP server that enables AI assistants to generate, score, and analyze DNA sequences using the evo2 genomic foundation model. It supports multiple execution modes including local GPU, SLURM clusters, and the Nvidia NIM cloud API for tasks like variant effect prediction and sequence embedding.

Enables AI assistants to perform DNA/RNA sequence alignment using BWA (Burrows-Wheeler Aligner), supporting both short and long read alignment to reference genomes with indexing, BWA-MEM, and BWA-backtrack algorithms.

Provides programmatic access to curated SNP data by trait, enabling LLM-powered applications to search, interpret, and discover genetic variants.

Provides GPU-accelerated scientific computing capabilities including symbolic mathematics, quantum wave mechanics simulations, molecular dynamics, and neural network training through four specialized MCP servers.

🔍 A biomedical literature annotation and relationship mining server based on PubTator3, providing convenient access through the MCP interface.

Enables installing, configuring, and running modular MCP servers for biology, bioinformatics, and bioimaging tasks, including local image analysis, ImageJ/Fiji bridging, and LLM-based agent workflows.

Enables real-time pharmacogenomics analysis, including variant clinical significance, drug-gene interactions, and dosing guidelines, by connecting to ClinVar, PharmGKB, gnomAD, and other databases.

Look up variant allele frequencies by ancestry, gene loss-of-function constraint, gene variant lists, and sequencing coverage over gnomAD — with ClinVar significance joined in — via MCP.

Enables querying relationships between plant species, small molecules, and mitochondrial Complex I inhibitors by bridging natural-product, biodiversity, and PubMed datasets. Allows LLMs to perform structured searches and reasoning over biological data to identify potential plant-derived mitochondrial inhibitors.

Provides a collection of MCP servers for computational chemistry tasks including molecular generation and retrosynthesis. Also offers property prediction and molecule pricing capabilities.

An MCP server that enables language models to fetch protein information from the UniProt database, including protein details, sequences, functions, and structures.

Search UniProtKB by protein function, fetch curated records, map IDs across databases, and pull reference proteomes, taxonomy, and sequences via MCP. Supports both STDIO and Streamable HTTP transports.