Alphafold Initial Guess

Predicts binder structure from sequence and an initial guess structure, initializing Alphafold with binder atoms to ensure proper binding during folding.

Quick Start

1. Prepare matching FASTA and PDB files (IDs must correspond).
2. Set desired parameters (e.g., recycles, monomer mode).
3. Run the node to generate predicted foldings and scores.

Setup Guide

1. Prepare Inputs

1. Ensure FASTA and PDB records have matching IDs for batch processing.
2. Adjust sequence and structure as needed for your design.

2. Configure Node

1. Set maintain_res_numbering to preserve residue numbering if required.
2. Adjust max_amide_dist, recycle, and force_monomer as needed.
3. Enable debug for strict error handling.

Basic Usage

Single or Batch Prediction

• Use for single or multiple sequence/structure pairs.
• Useful for binder design and initial structure refinement.

Configuration

Required Inputs

Field	Description	Type	Example
fasta	Sequences to run through the model. IDs must match PDBs for batch.	FASTA	">id1\nSEQUENCE"
pdb	Structures to run through the model. IDs must match FASTA for batch.	PDB	"{id1: pdb_content}"
maintain_res_numbering	Do not renumber residues on bad input.	BOOLEAN	False
max_amide_dist	Max distance between amide bond's carbon and nitrogen.	FLOAT	3.0
recycle	Number of AF2 recycles to perform.	INT	3
force_monomer	Predict structure as monomer.	BOOLEAN	False
debug	Crash on errors if True, continue otherwise.	BOOLEAN	True

Optional Inputs

None

Outputs

Field	Description	Example
folding.pdb	Predicted foldings.	"{id1: pdb_content}"
score.sc	Scores of the designs (rmsd, pae, plddt).	"rmsd: 1.2, plddt: 85"

Best Practices

Input Preparation

• Ensure FASTA and PDB IDs match for batch processing.
• Use high-quality initial structures for better results.

Parameter Tuning

• Adjust recycle for accuracy vs. speed.
• Use force_monomer for monomeric predictions only.

Troubleshooting

Common Issues

• Mismatched IDs: Ensure FASTA and PDB record IDs correspond exactly.
• Unexpected output: Check input formats and parameter values.

Need Help?

• Contact support for further assistance.