"Software or tools developed using Java" 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.

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

Provides protein family, domain, and functional annotation using InterProScan, supporting local or API backends.

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.

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.

MCP server that exposes the UniProt REST API to LLM clients, enabling search and retrieval of protein data via tools like search_uniprotkb, get_entry, and map_ids.

Enables AI-assisted molecular biology experiment design with tools for qPCR primer design, cloning strategy optimization, TaqMan probe design, and multiplex compatibility analysis.

A bridge connecting AI agents to NCBI's PubMed database through the Model Context Protocol, enabling seamless searching, retrieval, and analysis of biomedical literature and data.

Provides local DNA/RNA sequence analysis tools (composition, reverse complement, translation, ORF enumeration, motif scanning) via MCP for agent workflows.

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.

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

An MCP server for querying the KEGG bioinformatics database, providing tools, resource templates, and guided prompts for pathways, genes, compounds, and more.

MCP server for single-cell lineage tracing analysis, enabling conversational reconstruction, visualization, and heritability analysis of lineage trees using Cassiopeia, pycea, and treedata.