The AlphaFold glossary

“The worker machine”

A chain of amino acids that folds into a 3D shape.

“Bead”

One of 20 building blocks that make up proteins.

“Bead on the string”

A single amino acid once it is part of a protein chain.

“The origami”

How a chain of amino acids settles into its 3D shape.

“The spelling”

The linear order of amino acids.

“Spirals and ribbons”

Local shapes like α-helices and β-sheets.

“The whole knot”

The full 3D fold of one chain.

“The team-up”

How several chains assemble into a complex.

“The cooked spaghetti”

Part of a protein with no fixed shape.

“The family photo album”

Related sequences from other organisms lined up together.

“The synchronized dancers”

When two positions change together across species.

“The look-alike”

A known experimental structure of a similar protein.

“The seating chart”

A grid describing the relationship between every pair of residues.

“The gossip network”

AlphaFold 2's core block that mixes MSA and pair information.

“The group chat”

A neural network operation that lets each part look at all others.

“The three-way check”

A rule enforcing geometric consistency between residue triplets.

“The sculptor”

Turns abstract representations into 3D atom coordinates.

“The streamlined gossip”

AlphaFold 3's simplified replacement for the Evoformer.

“The fog clearer”

AlphaFold 3's generator that builds atoms by de-noising.

“The second draft”

Feeding the output back in for another pass.

“The answer model”

The 3D model AlphaFold produces.

“The shipping box”

The standard file format for 3D structures.

“The podium”

One of several predictions, sorted by confidence.

“The confidence thermometer”

Per-residue confidence score from 0 to 100.

“The distance doubt map”

How sure AlphaFold is about the relative position of two residues.

“The overall grade”

Overall confidence in the global fold (0–1).

“The handshake score”

Confidence in how chains in a complex fit together.

“The breakthrough”

DeepMind's 2020 breakthrough model for single chains.

“The teamwork edition”

Version of AlphaFold 2 trained for complexes.

“The generalist”

2024 model covering proteins, DNA, RNA, and small molecules.

“The ready-made library”

Free database of 200M+ predicted structures.

“The museum”

Protein Data Bank — archive of experimentally solved structures.

“The phone book”

The main database of protein sequences.

“The Olympics”

Biennial blind competition for structure prediction.