"A tool or software for blending or 3D modeling" 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.

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

Enables genomic sequence analysis through the Evo 2 model, supporting DNA sequence scoring, embedding, generation, and variant effect prediction with multiple model checkpoints (7B, 40B, 1B parameters).

Enables variant annotation and effect prediction using the Ensembl VEP API, with support for batch and single queries.

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.

Enables MCP hosts to run provenance-aware computational epitope research workflows, including sequence and immune-evidence analysis, structure and chemistry calculations, molecular docking, and checksummed 3D artifact exports.

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

Provides access to EMBL-EBI bioinformatics data including InterPro domains, Pfam families, protein features, and taxonomy through a unified tool.

A Model Context Protocol (MCP) server that provides access to the Protein Data Bank (PDB) - the worldwide repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies.

MCP server for biopharma software infrastructure offering FDA 21 CFR Part 11 audit trails, CDISC SDTM/Allotrope data exports, 4PL dose-response curve fitting, and HIPAA PII/PHI redaction through 10 Zod-validated tools.

Enables users to generate volcano plots by submitting jobs with input files and parameters, supporting local or Docker execution.

Enables searching ENA's public sequencing data by organism, study, platform, country or date, retrieving FASTQ/BAM download URLs and checksums, and discovering available result types and fields.

Enables AI agents to search EBI BioSamples metadata for biological samples such as cell lines, tissues, and organisms by free-text keyword, and to fetch individual records by accession to retrieve taxId, organism, and characteristics like tissue, sex, and cell type. It can run as a hosted gateway endpoint or locally over stdio via npx.

Enables AI agents to search public cancer genomics studies (TCGA, CPTAC, MSK, and more), fetch full details for individual studies, resolve gene symbols to Entrez ids, and list cancer types. Works keylessly against open cBioPortal data over a hosted MCP endpoint, a local stdio server, or plain HTTP.

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 agents to search protein family, domain, and functional-site entries, read entry metadata and clan relationships, map a UniProt protein's annotations to residue coordinates, and find proteins carrying a given signature. Runs over STDIO or Streamable HTTP with no credentials required.

Enables searching a manually curated database of stable macromolecular protein complexes by protein or complex name, gene, GO term, or biological process, and fetching individual records by accession to retrieve subunits with UniProt identifiers, biological roles, and stoichiometry. Complements UniProt, IntAct, and STRING, and can be used keyless over a hosted gateway endpoint or run locally over stdio.

MCP server for querying the GWAS Catalog (EBI/NHGRI), a curated catalog of genome-wide association studies. It enables AI agents to search and retrieve study data via natural language or direct tool calls.

Enables searching and retrieving cancer-genomics projects, cases, and genomic data files — including TCGA, TARGET, and CPTAC — via keyless, open-access metadata tools. Supports filtering by primary site, project, or data category, and can route plain-English questions to the right tool automatically.

Enables querying of the Monarch Initiative biomedical knowledge graph for genes, diseases, phenotypes, and their associations through natural language or direct tool calls.

Enables AI agents to resolve marine species names to OBIS taxon records, retrieve georeferenced ocean occurrence records with optional date filtering, and pull aggregate statistics such as record counts, contributing datasets, and observed year ranges. Queries the Ocean Biodiversity Information System keylessly over the Pipeworx gateway or as a local stdio server.

This server provides access to InterPro protein family, domain, and functional-site classification data from EBI. It allows querying protein annotations through natural language or direct tool calls.

Federates 13 gene-related MCP backends (gnomAD, GTEx, etc.) behind a single Streamable HTTP endpoint with collision-free namespacing and search-based tool discovery.

A Model Context Protocol server providing programmatic access to 3D protein structural data from RCSB PDB, PDBe, and UniProt, enabling search, retrieval, comparison, and analysis of protein structures.

Connects AI agents to a hosted remote MCP endpoint that searches academic papers, verifies references and retraction status, retrieves research datasets, grants, and biological or chemical data, and generates scientific figures across 50+ upstream sources. Supports OAuth sign-in with per-tool credit accounting, structured error reporting, and source attribution for results.

Lets Claude and ChatGPT open and drive a Spacewalk 3D chromatin viewer alongside the conversation.

Enables users to search and retrieve 3D cryo-EM and electron-tomography density maps by keyword or entry ID, returning details such as resolution, structure-determination method, sample, and release date.

Runs the full HyphAeon report and per-pillar analyses in-process, with MEME concordance, over stdio or streamable HTTP.

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

Enables AI agents to browse the Gene Ontology through the EBI QuickGO API, including keyword search for GO terms, retrieval of a term's name, aspect, definition and synonyms by id, and listing the GO annotations tied to a UniProt accession. Runs keyless over HTTP or as a local stdio server, with an optional gateway route that lets plain-English questions be answered without choosing tools manually.