"Integrating Claude code with Qwen or Gemini CLI tools for quality assurance" matching MCP servers:

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.

This server enables multi-agent conversations for interacting with Cirro's biological data platform through its OpenAPI interface, auto-generated using AG2's MCP builder.

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.

Predicts CRISPR gene dependencies and drug targets by integrating literature, regulatory/PPI networks, and genome-scale metabolic models.

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 read-only exploration of Copick cryo-ET projects and discovery/validation of copick CLI commands for building processing pipelines.

Enables querying the Human Protein Atlas data using natural language or direct MCP tools, with keyless access via the Pipeworx gateway.

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

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

A terminal-based bioinformatics CLI chat tool that integrates Ensembl VEP, NCBI ClinVar, an MCP server layer, and OpenRouter's NVIDIA Nemotron 3 Ultra model to provide variant consequence and clinical significance lookups with clear summaries in a Rich-powered CLI.

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.

Framework for building bioengineering automation tools that AI assistants can call via the Model Context Protocol, handling server registration and tool discovery automatically.

Enables Claude Code to interact with a TACC or SLURM HPC cluster for bioinformatics pipelines, allowing job management, log reading, file browsing, remote script execution, and job submission through natural language.

Manages local protein experiments with a Flask backend and SQLite, offering tools for protein library management, Beer-Lambert concentration calculations, BLI dilution planning, and experiment archiving. It provides 7 MCP tools for AI assistants like Claude to interact with the system.

An MCP server that grounds protein research in the UniProt SPARQL endpoint, providing tools for querying proteins, sequences, variants, diseases, and more via intent-named tools and raw SPARQL.

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 and Claude Plugin for a full ENCODE Project genomic data and analysis toolkit — search, download, track, and analyze functional genomics experiments