complexa-evaluate-pdbs

To evaluate PDB files for protein binder design, you can automate refolding and structural analysis workflows across directories. This process calculates complex interface metrics like i_pAE, pLDDT, and scRMSD to validate binder success rates against standard thresholds.

Yes, high-throughput PDB evaluation supports multiple folding backends including AlphaFold2 (AF2), RF3, ESMFold, and Boltz-2. You must configure your environment with access to one of these backends and the Proteina-Complexa CLI before running the workflow.

Monomer designability assessment uses comprehensive structural biology metrics to evaluate protein folding quality. The workflow computes complex interface metrics alongside monomer designability scores to provide consistent quality control across candidate batches.

No, you do not need to manually refold candidate protein binders. This automated workflow removes the manual burden of refolding and scoring large batches of protein or ligand binder designs, generating a summary CSV for the top-performing designs.

The best way to validate motif-ligand analysis for PDB structures is using an automated evaluation workflow. It orchestrates refolding and structural analysis to assess diverse scientific tasks, ensuring consistent quality control across your research pipeline.

Limitations of automating PDB evaluation include the strict requirement for a configured environment with access to specific folding backends and the Proteina-Complexa CLI. Without these dependencies properly configured, the structural analysis workflow cannot execute.