Simpkin Adam J, Elliot Luc G, Joseph Agnel Praveen, Burnley Tom, Stevenson Kyle, Sánchez Rodríguez Filomeno, Fando Maria, Krissinel Eugene, McNicholas Stuart, Rigden Daniel J, Keegan Ronan M
Institute of Structural, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom.
UKRI-STFC, Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom.
Acta Crystallogr D Struct Biol. 2025 Mar 1;81(Pt 3):105-121. doi: 10.1107/S2059798325001251. Epub 2025 Feb 20.
With the advent of next-generation modelling methods, such as AlphaFold2, structural biologists are increasingly using predicted structures to obtain structure solutions via molecular replacement (MR) or model fitting in single-particle cryogenic sample electron microscopy (cryoEM). Differences between the domain-domain orientations represented in a predicted model and a crystal structure are often a key limitation when using predicted models. 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 either Phaser, MOLREP or PowerFit. The slicing step can use the AlphaFold predicted aligned error (PAE) or can operate via a variety of C-atom-based clustering algorithms, extending the applicability to structures of any origin. The number of splits can either be selected by the user or determined automatically. Slice'N'Dice is available for both MR and automated map fitting in the CCP4 and CCP-EM software suites.
随着诸如AlphaFold2等下一代建模方法的出现，结构生物学家越来越多地使用预测结构，通过分子置换（MR）或在单颗粒低温样品电子显微镜（cryoEM）中进行模型拟合来获得结构解决方案。在使用预测模型时，预测模型中表示的结构域-结构域方向与晶体结构之间的差异通常是一个关键限制。Slice'N'Dice是一个软件包，旨在通过首先将模型切割成不同的结构单元，然后使用Phaser、MOLREP或PowerFit自动放置切片来解决这个问题。切割步骤可以使用AlphaFold预测对齐误差（PAE），也可以通过各种基于C原子的聚类算法进行操作，从而将适用性扩展到任何来源的结构。分割的数量可以由用户选择或自动确定。Slice'N'Dice可用于CCP4和CCP-EM软件套件中的MR和自动图谱拟合。
