"Tools to Enhance Code Quality and Organization with Claude in Cursor" matching MCP servers:

Control PyMOL from Cursor via natural language. Enables describing molecular structures and styles in plain language to execute PyMOL commands through XML-RPC.

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

Enables 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.

A 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.

Enables searching cryo-EM density maps in EMDB and raw datasets in EMPIAR, with filtering by resolution, keyword, and cross-referencing between the two databases.

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.

Enables researchers to query public ENA and BioSamples genomics data in plain English through any MCP client, including counting records, searching samples, retrieving sample details, and checking metadata quality against project requirements.

Run real bioinformatics from your AI agent on your own GPUs: MMseqs2 homology search, ESMFold structure prediction and sequence tools for Claude, Cursor and Codex. GPU-aware scheduling for shared machines, fail-fast input checks, background jobs, agent-friendly results and provenance for every run.

Exposes a bio-hybrid neuromorphic simulation pipeline (SNN, consciousness proxies, FinalSpark NeuroPlatform) as MCP tools, resources, and prompts for AI assistants like Claude, Cursor, and VS Code.

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.

Exposes the Adaptyv Foundry protein characterization API as MCP tools, enabling AI assistants to interact with experiments, targets, sequences, and results in natural language.

An MCP server for running local LLMs using llama-cpp-python, with built-in tools for generating drug-like molecule SMILES.

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

Enables automated cell type annotation in scRNA-seq analysis using CellTypist models, with tools for listing, downloading, training, and annotating cell types via natural language.

Resolves free-text condition and disease strings — trial-registry condition fields, drug-label indications, hand-typed wording — onto the Mondo Disease Ontology, returning the best term id and label along with a trustworthy match-quality label (exact label/synonym, broader, narrower, fuzzy, or no-match) plus cross-ontology xrefs. Optionally expands a resolved term to all of its descendant ids for building subtype-inclusive registry filters.

Enables AI agents to retrieve and analyze breeding data from BrAPI-compliant databases through shared tools, with human-in-the-loop approval and verification.

A professional MCP server for comprehensive bioinformatics quality control, providing automated FastQC/MultiQC analysis, HTML report parsing, and advanced data visualization for sequencing data.

Enables AI assistants to query VCF files through MCP tools that summarize variants, identify pathogenic and carrier variants, interpret pharmacogenomic results, and determine APOE status, with web app and Claude Desktop support.

BioOpenMCP enables users to run bioinformatics tools like FastQC, Cutadapt, and STAR with background execution and status checking. It integrates with Claude Desktop to perform quality control, trimming, alignment, and reporting via natural language.

Enables LLMs and AI agents to query a biomedical knowledge graph stored in RedisGraph, with tools for concept search, synonym enrichment, and study variable discovery through semantic relationships.