MSA Structure Prediction Pipeline

Predict protein structures with high accuracy by chaining two BioNeMo NIMs:

Step 1: MSA-Search  →  Step 2: OpenFold3
(Search homologs)       (Predict structure with MSA)

Overview

Why chain these NIMs?

• MSA-Search finds evolutionary homologs in UniRef30 and ColabFold databases using GPU-accelerated MMSeqs2. The resulting alignment provides crucial evolutionary information.
• OpenFold3 uses the MSA to improve structure prediction accuracy — especially for sequences where no close homolog exists in PDB.
• Running MSA-Search first means OpenFold3 gets the full evolutionary context rather than a single-sequence prediction.