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Colabfold Search

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Performs Colabfold MSA search on provided protein sequences against known sequence databases, returning results for each sequence in .a3m format as a dictionary {seq_id: a3m_content}.

Quick Start

  1. Prepare your protein sequences in FASTA format.
  2. Connect the FASTA input to the Colabfold Search node.
  3. Run the node to obtain MSA search results in .a3m format.

Setup Guide

1. Prepare Input

  1. Format your protein sequences as a valid FASTA string.
  2. Ensure each sequence has a unique identifier.
  1. Connect the FASTA input to the node.
  2. Execute the node to perform the MSA search.

Basic Usage

  • Accepts single or multiple protein sequences in FASTA format.
  • Returns a dictionary mapping each sequence ID to its .a3m MSA result.

Configuration

Required Inputs

Field Description Type Example
fasta Sequences to run Colabfold MSA search on. FASTA ">seq1\nMKT..."

Optional Inputs

None

Outputs

Field Description Example
msa.a3m Search results as a dict {seq_id: a3m_content}. { "seq1": "...a3m..." }

Best Practices

Input Preparation

  • Use clear, unique sequence IDs in your FASTA records.
  • Validate FASTA formatting to avoid processing errors.

Workflow Integration

  • Use the output .a3m directly as input for downstream structure prediction nodes (e.g., Alphafold, Boltz).
  • For batch processing, ensure all sequences are relevant to the same analysis context.

Troubleshooting

Common Issues

  • Empty or malformed FASTA input: Ensure your input is properly formatted and not empty.
  • Timeouts on large batches: For very large numbers of sequences, consider splitting into smaller batches.

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