Glossary¶
Quick reference for every acronym and term used across this guide. Each entry links to the page where it's actually explained in depth — this page is for looking something up mid-read, not for learning it the first time.
- AlphaFold-Multimer
- The complex/multi-chain prediction mode of AlphaFold2. See AlphaFold-Multimer version history.
- AlphaMissense
- A separate DeepMind model, built on AlphaFold2's architecture, that scores human missense variants for likely pathogenicity. See What is AlphaMissense?
- BFD (Big Fantastic Database)
- The largest of the sequence databases AlphaFold2/ColabFold search for MSA construction — dominates the ~2.6 TB database bundle size. See Running ColabFold (local/HPC).
- Evoformer
- AlphaFold2's central trunk network — 48 blocks jointly refining the MSA and pair representations. See How AlphaFold Works.
- Foldseek
- A structure-search tool that finds structural homologs by converting structures into a "3Di" structural alphabet — far more sensitive than sequence search for distant relatives. See Structure vs. Sequence Homology and the ChopChopMF Foldseek workflow.
- IDR (Intrinsically Disordered Region)
- A part of a protein with no single fixed 3D structure — better described as a conformational ensemble. Frequently shows low pLDDT. See Confidence Metrics.
- ipTM (interface predicted TM-score)
- A 0–1 confidence score for the interface between chains in a predicted complex — the single most useful number for "is this predicted interaction believable?" See pTM and ipTM.
- MSA (Multiple Sequence Alignment)
- An alignment of many homologous sequences to a query — the dominant source of information AlphaFold uses to predict structure. See How AlphaFold Works and What Actually Influences a Prediction?.
- PAE (Predicted Aligned Error)
- A pairwise, per-residue-pair confidence measure in Ångströms — how sure AlphaFold is about the relative position of two residues. See PAE — Predicted Aligned Error.
- Pairformer
- AlphaFold3's trunk network, replacing the Evoformer — keeps the pair/single representations but uses a much lighter MSA module. See How AlphaFold Works.
- PDE (Predicted Distance Error)
- An AlphaFold3-specific confidence metric — pairwise distance accuracy independent of frame alignment, related to but distinct from PAE. See Confidence Metrics.
- pLDDT (predicted Local Distance Difference Test)
- A 0–100 per-residue (or, in AF3, per-atom) confidence score. See pLDDT — per-residue local confidence.
- pTM (predicted TM-score)
- A 0–1 confidence score summarizing the accuracy of an entire predicted fold in one number. See pTM and ipTM.
- PTM (Post-Translational Modification)
- A biochemical modification made to a protein after translation (phosphorylation, glycosylation, etc.) — not modeled at all by AlphaFold2, but explicitly supported as input by AlphaFold3. See What Actually Influences a Prediction?.
- Recycling
- Feeding AlphaFold's own output back into the start of the trunk network for multiple refinement passes. See How AlphaFold Works.
- Remote homology
- A relationship between two proteins that share a common ancestor so distant that sequence alignment can no longer detect it, even though structure still can. See Structure vs. Sequence Homology.
- Twilight zone
- The pairwise sequence-identity range (roughly below 20–25%) where sequence-alignment scores become statistically indistinguishable from chance. See Structure vs. Sequence Homology.
Missing a term? This guide is a living document — see Resources & Further Reading for the primary sources everything here is drawn from.