AlphaFold pLDDT and expected distance error: Difference between revisions

The pLDDT value (reload <scene name='92/920232/One_dimensional/1'>initial scene</scene>) is assigned to each individual residue (or atom<ref name="af3faq" />) and stored in predicted [[atomic coordinate file]]s instead of [[temperature|temperature factors]]. This value is named pLDDT because it predicts the so-called LDDT value (Local Distance Difference Test, <ref>PMID: 23986568</ref>), a way to characterize the difference of two related conformations without aligning the structures. Different from temperature factors, high values indicate high confidence in atomic positions, and low values low confidence (scale of 0 to 100). Programs such as [[FirstGlance in Jmol]] and [[iCn3D]] automatically reverse the usual temperature color scheme, coloring high confidence blue, and low confidence red.