lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests.
- Mariani V Biozentrum, Universität Basel, Klingelbergstrasse 50-70 and Computational Structural Biology, SIB Swiss Institute of Bioinformatics, 4056 Basel, Switzerland.
- Biasini M
- Barbato A
- Schwede T
- 2013-08-30
Published in:
- Bioinformatics (Oxford, England). - 2013
Computational Biology
Models, Molecular
Protein Conformation
Protein Folding
Protein Structure, Tertiary
Proteins
Software
Stereoisomerism
English
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 α 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 superposition-free 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.
AVAILABILITY AND IMPLEMENTATION
Source code, binaries for Linux and MacOSX, and an interactive web server are available at http://swissmodel.expasy.org/lddt.
CONTACT
torsten.schwede@unibas.ch.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
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 α 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 superposition-free 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.
AVAILABILITY AND IMPLEMENTATION
Source code, binaries for Linux and MacOSX, and an interactive web server are available at http://swissmodel.expasy.org/lddt.
CONTACT
torsten.schwede@unibas.ch.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
- Language
-
- English
- Open access status
- hybrid
- Identifiers
-
- DOI 10.1093/bioinformatics/btt473
- PMID 23986568
- Persistent URL
- https://folia.unifr.ch/global/documents/246503
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