"using-the-internet-for-searches" matching MCP servers:

An MCP server that provides tools for searching and fetching protein data from the UniProt database using the unipressed library.

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

Enables protein structure and sequence searches using FoldSeek, with support for multiple databases, automatic model downloads, and structured job management.

Provides seamless access to the Protein Data Bank in Europe (PDBe) API and search capabilities, enabling AI clients to query protein structures, perform advanced searches, and retrieve structural biology data.

A Model Context Protocol server that enhances language models with protein structure analysis capabilities, enabling detailed active site analysis and disease-related protein searches through established protein databases.

Enables AI assistants to perform NCBI BLAST sequence similarity searches through natural language, supporting nucleotide and protein searches, custom database creation, and multiple output formats.

Enables complex searches, sequence mapping, genomic analysis, and metadata retrieval for non-coding RNA sequences from the RNAcentral database.

Provides a natural language interface for scRNA-Seq analysis using the Scanpy library, supporting operations such as data preprocessing, clustering, and visualization. It enables AI agents and clients to perform complex single-cell transcriptomics workflows through the Model Context Protocol.

Enables querying and retrieving bacterial and viral genomic data, features, antimicrobial resistance, and epitopes from the BV-BRC API using natural language.

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

Validates the physical and chemical plausibility of ligand–protein docking poses using the PoseBusters tool.

Enables AI assistants to explore VEuPathDB WDK catalogs, searches, parameters, and gene data, and to perform gene lookups, expression summaries, step estimates, and download URL retrieval using VEuPathDB credentials.

Searches UniProt by protein name to find accession numbers and retrieves detailed protein structure information from AlphaFold, including direct links to 3D structural predictions.

Reproduces the in-silico toxicological profile of Heracleum sosnowskyi metabolites from Rassabina & Fedorov (2025) using open-source models for LD50 prediction, toxicity classification, chemical space clustering, and synthesis cost estimation.

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.

Provides a natural language interface for single-cell RNA-Seq analysis using the decoupleR framework. It enables users to perform biological pathway inference, data clustering, and visualization through MCP-compatible AI clients.

Wraps NCBI BLAST+ blastp into a FastMCP service for auditable protein homology searches with local output artifacts and structured metadata.

Enables protein modeling and design using the Rosetta suite via Docker, including structure refinement, mutation stability analysis, docking, and loop modeling through natural language commands.

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 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.