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Here are pages in Proteopedia that relate to AlphaFold. | Here are pages in Proteopedia that relate to AlphaFold. | ||
==Introductions to AlphaFold== | |||
*[[AlphaFold]]. An introduction and overview. | *[[AlphaFold]]. An introduction and overview. | ||
*[[Theoretical models]] describes the breakthrough in structure prediction made by AlphaFold in [[CASP]] 14 (2020) and the continued pre-eminence of AlphaFold in CASP 15 [2022]. | |||
==How To Make Predictions== | |||
*[[How to predict structures with AlphaFold]] when the [https://alphafold.ebi.ac.uk/ AlphaFold Database] does not already have what you want. | *[[How to predict structures with AlphaFold]] when the [https://alphafold.ebi.ac.uk/ AlphaFold Database] does not already have what you want. | ||
*[[Joining AlphaFold predictions for halves of a molecule]], when the sequence is too long for AlphaFold to handle. | *[[Joining AlphaFold predictions for halves of a molecule]], when the sequence is too long for AlphaFold to handle. | ||
*[[AlphaFold2 examples from CASP 14]]. A detailed analysis of several AlphaFold predictions compared with [[Empirical models|empirically-determined structures]]. | *[[How to renumber PDB files]] in order to correct sequence numbers. | ||
==Interpreting Predictions== | |||
*[[AlphaFold pLDDT and expected distance error]] | |||
*[[FirstGlance/How_to_get_average_pLDDT_from_AlphaFold_models|How to get average pLDDT from AlphaFold models]]: When any subset of residues (such as a sequence range) is selected (using <i>Find</i>) in [[FirstGlance in Jmol]], listing the found residues reports their average pLDDT. | |||
*[[Calculating GDT TS]] the Global Distance Test Total Score, one of the metrics used for judging accuracy of predictions in the [[CASP]] competitions. | |||
*[[User:Eric Martz/AlphaFold3 case studies|AlphaFold3 case studies]] includes a case that AlphaFold3 cannot predict. | |||
==Examples of Predictions== | |||
*[[AlphaFold2 examples from CASP 14]]. A detailed 2021 analysis of several AlphaFold predictions compared with [[Empirical models|empirically-determined structures]]. | |||
*[[User:Eric Martz/AlphaFold3 case studies|AlphaFold3 case studies]] (November 2024) includes a case that AlphaFold3 cannot predict. | |||
==Uses of Predictions== | |||
*[[Missing residues and incomplete sidechains]] suggests using AlphaFold predicted structures, in parallel with [[empirical models]] that have missing residues or atoms, when analyzing surface characteristics such as charge distribution ([[electrostatic potential maps]]), [[salt bridges]], [[cation-pi interactions]], etc. | |||
*[[Converting AlphaFold3 CIF to PDB]] | |||
==See Also== | |||
*[[RoseTTAFold]] | |||
*[[wwPDB]], the WorldWide Protein DataBank archive of [[empirical models]]. | |||
*[[ModelArchive]], a database of theoretical (non-empirical) models. | |||
