Slice’N’Dice: Maximising the value of predicted models for structural biologists

By Adam J. Simpkin, Luc Elliott, Kyle Stevenson, Eugene Krissinel, Daniel J. Rigden, Ronan M. Keegan. 2022

6 citations recorded by the source corpus.

With the advent of next generation modelling methods, such as AlphaFold2, structural biologists are increasingly using predicted structures as search models for Molecular Replacement (MR) when experimental structures of homologues are unavailable. Inaccuracy in domain-domain orientations is often a key limitation when using predicted models for MR. Slice’N’Dice is a software package designed to address this issue by first slicing models into distinct structural units and then automatically placing the slices using Phaser. The slicing step can use AlphaFold2’s predicted aligned error (PAE), or can operate via a variety of Cα atom clustering algorithms, extending applicability to structures of any origin. The number of splits can be selected by the user. Slice’N’Dice is available in CCP4 8.0 and is currently being adapted for cryo-EM use cases.

Subfields: Materials Chemistry, Molecular Biology, Pharmacology

Citations in the corpus