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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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"Tools and resources for PDF and XML document processing" 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
- -license-quality-maintenanceThis server enables multi-agent conversations for interacting with Cirro's biological data platform through its OpenAPI interface, auto-generated using AG2's MCP builder.
- AlicenseAqualityFmaintenanceAn MCP server that enables AI coding assistants to interact with Rosetta, PyRosetta, and Biotite for running RosettaScripts, validating XML, translating between Rosetta and Biotite, scoring structures, and querying documentation.1911218MIT
- AlicenseAqualityCmaintenanceConnects 3D Slicer with AI assistants through the Model Context Protocol, enabling medical image processing and scene manipulation using natural language.338MIT
- AlicenseBqualityAmaintenanceEnables running GROMACS molecular dynamics simulations through natural language, with tools for topology building, solvation, simulation management, and trajectory processing via the Model Context Protocol.31MIT
- AlicenseCqualityCmaintenanceAn MCP server that enables single-cell RNA sequencing analysis through natural language, supporting data processing, visualization, and analysis tasks without requiring coding knowledge.5212BSD 3-Clause
- AlicenseCqualityCmaintenanceExposes 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.49MIT
Copick MCP Serverofficial
Alicense-qualityCmaintenanceEnables read-only exploration of Copick cryo-ET projects and discovery/validation of copick CLI commands for building processing pipelines.MIT- Alicense-qualityCmaintenanceAn MCP server that wraps R scripts for microbiome and amplicon (16S/ITS) analysis, providing tools for alpha/beta diversity, differential abundance, networks, and more, with PNG/PDF outputs.MIT
- Alicense-qualityDmaintenanceProvides chemical informatics endpoints for converting between chemical names and SMILES, processing molecule structures, and comparing molecules, with MCP compatibility.4MIT
- Alicense-qualityFmaintenanceExecutes SPARQL queries against biological and biomedical RDF databases from the RDF Portal, with additional REST API integrations for bioinformatics resources.1MIT
- Alicense-qualityDmaintenanceA unified MCP server for biomedical research that connects AI systems to resources like Ensembl, EuropePMC, STRING, and more, enabling retrieval of verified domain-specific information.Apache 2.0
- Flicense-qualityDmaintenanceControl PyMOL from Cursor via natural language. Enables describing molecular structures and styles in plain language to execute PyMOL commands through XML-RPC.1
- Flicense-qualityCmaintenanceEnables RNA structure analysis, sequence evaluation, and inverse design using geometric deep learning models. Supports both quick computational analysis and long-running batch processing for generating RNA sequences that fold into target structures.
- Flicense-qualityCmaintenanceProvides access to the AlphaFold Protein Structure Database with tools for structure retrieval, confidence analysis, batch processing, and visualization.
- Flicense-qualityDmaintenanceEnables protein sequence analysis and structure prediction by extracting ESM-2 embeddings and batch processing FASTA files via Docker. It provides tools for large-scale embedding extraction, job monitoring, and model management within an MCP-compatible environment.
- Flicense-qualityDmaintenanceEnables protein structure prediction using the Chai-1 model via Docker, with tools for small peptides, FASTA-based predictions, MSA-enhanced predictions, batch processing, and job management.