Federated protein structure & annotation across experimental (PDB) and predicted (AlphaFold) models via MCP. STDIO or Streamable HTTP.
Setup
Choose your client, copy the config, then fill in any required environment variables.
Local
claude mcp add protein -- npx -y protein-mcp-server~/.codex/config.toml
[mcp_servers.protein]
command = "npx"
args = ["-y", "protein-mcp-server"]
# codex mcp add protein -- npx -y protein-mcp-server~/.cursor/mcp.json
{
"mcpServers": {
"protein": {
"command": "npx",
"args": [
"-y",
"protein-mcp-server"
]
}
}
}.vscode/mcp.json
{
"servers": {
"protein": {
"type": "stdio",
"command": "npx",
"args": [
"-y",
"protein-mcp-server"
]
}
}
}~/.gemini/settings.json
{
"mcpServers": {
"protein": {
"command": "npx",
"args": [
"-y",
"protein-mcp-server"
]
}
}
}claude_desktop_config.json
{
"mcpServers": {
"protein": {
"command": "npx",
"args": [
"-y",
"protein-mcp-server"
]
}
}
}.trae/mcp.json
{
"mcpServers": {
"protein": {
"command": "npx",
"args": [
"-y",
"protein-mcp-server"
]
}
}
}Remote
claude mcp add --transport http protein https://protein-mcp-server--cyanheads.run.tools~/.codex/config.toml
[mcp_servers.protein]
url = "https://protein-mcp-server--cyanheads.run.tools"
# codex mcp add protein --url https://protein-mcp-server--cyanheads.run.tools~/.cursor/mcp.json
{
"mcpServers": {
"protein": {
"url": "https://protein-mcp-server--cyanheads.run.tools"
}
}
}.vscode/mcp.json
{
"servers": {
"protein": {
"type": "http",
"url": "https://protein-mcp-server--cyanheads.run.tools"
}
}
}~/.gemini/settings.json
{
"mcpServers": {
"protein": {
"httpUrl": "https://protein-mcp-server--cyanheads.run.tools"
}
}
}claude_desktop_config.json · Customize › Connectors › Add custom connector
{
"mcpServers": {
"protein": {
"command": "npx",
"args": [
"-y",
"mcp-remote",
"https://protein-mcp-server--cyanheads.run.tools"
]
}
}
}.trae/mcp.json
{
"mcpServers": {
"protein": {
"url": "https://protein-mcp-server--cyanheads.run.tools"
}
}
}