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PDB To Fasta

Extracts FASTA-formatted amino acid sequences from the provided PDB record, supporting extraction for specific chains or all chains in the structure.

PDB To Fasta

Quick Start

  1. Connect a PDB input (single or batch) to the node.
  2. Specify chain IDs as a comma-separated string (e.g., A,B), or leave empty to extract all chains.
  3. Run the node to obtain FASTA sequences for each chain.

Setup Guide

1. Prepare Input

  1. Ensure your PDB input is a valid dictionary {pdb_id: pdb_content}.
  2. Identify the chain(s) you wish to extract (e.g., A, B, or leave empty for all).

2. Node Configuration

  1. Set the chains field to the desired chain IDs (comma-separated), or leave empty for all chains.
  2. Connect the node in your workflow.

Basic Usage

Extracting FASTA from a Single Chain

  • Provide a PDB with a single chain and specify its ID in chains (e.g., A).
  • The output will be a FASTA record for that chain.

Extracting FASTA from Multiple Chains

  • Provide a PDB with multiple chains and specify multiple IDs (e.g., A,B).
  • The output will include a FASTA record for each specified chain.

Configuration

Required Inputs

Field Description Type Example
pdb Protein to extract FASTA from. PDB {"1abc": "...PDB content..."}
chains Comma-separated chain IDs, or empty for all. STRING A,B

Optional Inputs

None

Outputs

Field Description Example
seqs.fasta FASTA records (sequence per chain) extracted from PDB. >1abc_chain_A\nMKT...

Best Practices

Input Preparation

  • Ensure PDB input is properly formatted and contains valid chain IDs.
  • Use unique PDB IDs to avoid confusion in batch processing.

Chain Selection

  • Specify only the chains you need to minimize unnecessary output.
  • Leave chains empty to extract all available chains if unsure.

Troubleshooting

Common Issues

  • No valid protein sequences found in the PDB: Ensure the PDB contains standard amino acid residues and correct chain IDs.
  • Empty output: Check that the specified chains exist in the input PDB.

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