lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests.

Motivation: The assessment of protein structure prediction techniques requires objective criteria to measure the similarity between a computational model and the experimentally determined reference structure. Conventional similarity measures based on a global superposition of carbon alpha atoms are strongly influenced by domain motions and do not assess the accuracy of local atomic details in the model. Results: The Local Distance Difference Test (lDDT) is a superpositionfree score that evaluates local distance differences of all atoms in a model, including validation of stereochemical plausibility. The reference can be a single structure, or an ensemble of equivalent structures. We demonstrate that lDDT is well suited to assess local model quality, even in the presence of domain movements, while maintaining good correlation with global measures. These properties make lDDT a robust tool for the automated assessment of structure prediction servers without manual intervention.