"X++ Programming Language (Microsoft Dynamics AX)" matching MCP servers:

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.

Integrates the miEAA 3.x bioinformatics platform with Claude Desktop, enabling microRNA enrichment analysis, identifier conversion between miRBase versions, and miRNA-precursor transformations through natural language.

Enables running GROMACS molecular dynamics simulations through natural language, with tools for topology building, solvation, simulation management, and trajectory processing via the Model Context Protocol.

Enables AI agents to control RELION 5.x cryo-EM structure determination software through natural language, providing 23 tools for the complete single-particle analysis pipeline.

Enables LLM agents to design proteins, predict structures, score interfaces, and run molecular dynamics simulations through a unified interface.

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 Model Context Protocol server that enables AI assistants to interact with LAMMPS for molecular dynamics simulations through natural language commands.

Integrates GROMACS molecular dynamics simulations with VMD visualization, enabling setup, execution, analysis, and 3D visualization of molecular dynamics workflows through natural language.

Enables LLMs to run rule-based molecular interaction simulations using the Kappa language through the Kappybara package. Returns simulation results as CSV data for analysis of biochemical systems and molecular binding dynamics.

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.

Enables DNA sequence analysis and variant effect prediction using Evo2-7B via MCP tools, providing forward inference, likelihood scoring, and batch variant comparison through natural language.

Enables analysis of bulk RNA-seq data using natural language queries, executing R and Python in a Docker container with automatic sample anonymization and privacy controls.

An MCP server that interfaces with Gigwa for genotyping data import, analysis, and audit, enabling users to perform complex workflows through natural language commands.

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 agents to search a public PubMed-derived corpus by natural language or identifiers and to retrieve publication details while traversing bounded citation and semantic literature graphs.

Enables AI assistants to search, browse, and retrieve interactive cell images and subcellular location data, including cell types, SVG illustrations, and location details through natural-language tool calls.

Connects 3D Slicer with AI assistants through the Model Context Protocol, enabling medical image processing and scene manipulation using natural language.

Enables querying the WormBase database for C. elegans and nematode genomics data, including gene information, protein sequences, phenotypes, interactions, and expression patterns through natural language.

Enables AI assistants to query the eggNOG 7 database in natural language for protein lookups, orthologous groups, pairwise orthologs, protein families, taxonomy, and database statistics. Also delivers structured functional annotations such as KEGG KO and GO terms with confidence scores, plus an index of bulk-downloadable data files.

Provides an MCP interface to the ROBOT command-line tool for OWL ontology editing, enabling operations like merging, reasoning, and conversion via natural language.