molclaw-proteinmpnn-tool

What problem does it solve?

Enables automated design and scoring of protein sequences directly from PDB structures to accelerate structure-guided sequence engineering workflows and reduce manual pipeline orchestration.

Core Features & Use Cases

• Structure-guided sequence design: Generate multiple candidate sequences per target using ProteinMPNN model variants with options for CA-only or soluble weights.
• Scoring and validation integration: Run scoring-only mode against provided FASTA inputs and incorporate downstream structure prediction (e.g., ESMFold) for self-consistency checks.
• Constraint-aware design: Support chain-specific redesign, fixed/designable residue positions, homooligomer tied positions, amino-acid omission/bias controls, and deterministic seeding for reproducibility.
• Use Case: Batch-design 8 sequences for each chain in a screening set of PDB files, verify produced counts, and fetch predicted structures for validation.

Quick Start

Design eight sequences for chain A from the uploaded PDB file /path/to/input.pdb using model v_48_020 with sampling temperature 0.1 and dry_run set to False.