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maintenanceProvides a collection of MCP servers for computational chemistry tasks including molecular generation and retrosynthesis. Also offers property prediction and molecule pricing capabilities.
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"Popular MCP tools commonly used by programmers" matching MCP servers:
- Alicense-qualityDmaintenanceEnables deep probabilistic analysis of single-cell omics data using scvi-tools through natural language. Supports SCVI for scRNA-seq analysis, SCANVI for cell type annotation, TOTALVI for multi-modal RNA/protein data, and PEAKVI for scATAC-seq analysis.MIT
- Alicense-qualityDmaintenanceA specialized MCP server for Metal-Organic Framework research that provides tools for database searching, structural optimization, and energy calculations via ASE. It enables scientific workflows by allowing users to interact with MOF data and perform chemical simulations through a standard SSE interface.MIT
- Alicense-qualityCmaintenanceEnables searching cryo-EM density maps in EMDB and raw datasets in EMPIAR, with filtering by resolution, keyword, and cross-referencing between the two databases.MIT
- AlicenseAqualityBmaintenanceMCP 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.11MIT
- AlicenseBqualityFmaintenanceEnables molecular design and simulation through 45 chemistry tools including pKa calculations, geometry optimization, conformer searches, docking, protein cofolding, and ADMET predictions powered by Rowan's computational chemistry platform.4123MIT
- AlicenseBqualityDmaintenanceEnables AI assistants to access protein information directly from UniProt, allowing retrieval of protein names, functions, sequences, and organism data by accession number.214MIT
Bio-MCP BLASTofficial
Alicense-qualityDmaintenanceEnables AI assistants to perform NCBI BLAST sequence similarity searches through natural language, supporting nucleotide and protein searches, custom database creation, and multiple output formats.10MITBio-MCP FastQC Serverofficial
Alicense-qualityDmaintenanceEnables 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.MITbio-mcp-evo2official
Alicense-qualityDmaintenanceAn 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.MIT
galaxy-mcpofficial
Alicense-qualityAmaintenanceMCP 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.37MIT- Alicense-qualityDmaintenanceExposes the Adaptyv Foundry protein characterization API as MCP tools, enabling AI assistants to interact with experiments, targets, sequences, and results in natural language.MIT
- Alicense-qualityBmaintenanceExposes pipen bioinformatics pipelines as MCP tools, allowing AI assistants to discover and run complex workflows through a progressive disclosure interface.1MIT
- Alicense-qualityDmaintenanceAn MCP server for running local LLMs using llama-cpp-python, with built-in tools for generating drug-like molecule SMILES.3MIT
- Alicense-qualityDmaintenanceEnables 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.MIT
- Alicense-qualityDmaintenanceProvides programmatic access to curated SNP data by trait, enabling LLM-powered applications to search, interpret, and discover genetic variants.MIT
- Alicense-qualityCmaintenanceEnables querying Ensembl genomic data including gene lookup, sequence retrieval, homology, variation, and variant effect prediction via MCP tools.12MIT
- Alicense-qualityDmaintenanceEnables real-time pharmacogenomics analysis, including variant clinical significance, drug-gene interactions, and dosing guidelines, by connecting to ClinVar, PharmGKB, gnomAD, and other databases.1MIT
- Alicense-qualityAmaintenanceLook 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.541Apache 2.0
- Alicense-qualityCmaintenanceProvides tools to query and resolve identifiers from the Bioregistry, including prefix metadata, CURIE resolution, and substring search.9MIT