pharmaclaw-alphafold-agent

name

pharmaclaw-alphafold-agent

description

Compliant AlphaFold Agent for protein structure retrieval, ESMFold prediction, binding site detection, and RDKit ligand docking. Fetches public PDB/AlphaFold DB structures, predicts folds via ESMFold (HuggingFace), identifies binding pockets, and performs basic molecular docking. Chains from Chemistry Query (receives SMILES for docking) and feeds into IP Expansion and Catalyst Design. Triggers on alphafold, fold, PDB, docking, structure, protein, binding site, pocket, UniProt, KRAS, target.

PharmaClaw AlphaFold Agent

Overview

Protein structure retrieval and ligand docking agent for the PharmaClaw drug discovery pipeline. Fetches experimental structures from RCSB PDB and predicted structures from AlphaFold DB, detects binding sites, and performs conformer-based docking with RDKit.

Quick Start

# Fetch structure and dock a ligand
python scripts/alphafold_agent.py '{"uniprot": "P01116", "smiles": "CC(=O)Nc1ccc(O)cc1"}'

# Structure retrieval only
python scripts/alphafold_agent.py '{"uniprot": "P01116"}'

Capabilities

Feature	Method	Source
Structure Fetch	RCSB Search API + AlphaFold DB	Public PDB files
Fold Prediction	ESMFold via HuggingFace	Sequence → 3D structure
Binding Sites	Pocket detection	Residue-level pockets
Ligand Docking	RDKit conformer generation	SMILES → affinity score

Decision Tree

• UniProt ID provided? → Fetch from RCSB PDB / AlphaFold DB
• → Predict fold via ESMFold