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structural-alignment

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Align protein structures using Foldseek 3Di, TM-align, US-align, DALI, or Foldmason for structural MSA. Predict, score, and superpose backbone coordinates when sequence identity is below the twilight zone or remote-homology detection is required. Use when sequence MSA fails (<25% identity), when the dark proteome is the target, when AlphaFoldDB / ESM Atlas search is needed, or when structural superposition is the goal.

When to use

• | Sequence identity | Recommended approach | |-------------------|---------------------| | >= 40% | Sequence DP (Bio.Align, BLASTP) is sufficient | | 25-40% | Sensitive sequence (MMseqs2, jackhmmer, profile-profile HHsearch) | | 15-25% | P…

When not to use

• Sequence identity >= 40%
• Sequence identity 25-40% (sensitive sequence methods preferred)

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