Table 4 Comparison of major protein modeling tasks

From: Flow matching meets biology and life science: a survey

Task

Input

Output

Objective

Protein structure prediction

Amino acid sequence

Full 3D structure (backbone + side chains)

Predict natural folded conformation

Protein design

Target structure or functional constraint

Amino acid sequence (or full structure)

Design a sequence that folds into a desired structure or achieves a function

Protein backbone generation

Partial structure, constraints, or motifs

Backbone atomic coordinates (N, Cα, C)

Generate realistic backbone conformations as design templates

  1. We highlight the distinctions in input, output, objective, and representative methods.
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