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Nucleic Acids Res. 2014 Jul;42(Web Server issue):W259-63. doi: 10.1093/nar/gku294. Epub 2014 May 16.

The CAD-score web server: contact area-based comparison of structures and interfaces of proteins, nucleic acids and their complexes.

Author information

1
Institute of Biotechnology, Vilnius University, Graičiūno 8, Vilnius LT-02241, Lithuania Faculty of Mathematics and Informatics, Vilnius University, Naugarduko 24, Vilnius LT-03225, Lithuania.
2
Institute of Biotechnology, Vilnius University, Graičiūno 8, Vilnius LT-02241, Lithuania venclovas@ibt.lt.

Abstract

The Contact Area Difference score (CAD-score) web server provides a universal framework to compute and analyze discrepancies between different 3D structures of the same biological macromolecule or complex. The server accepts both single-subunit and multi-subunit structures and can handle all the major types of macromolecules (proteins, RNA, DNA and their complexes). It can perform numerical comparison of both structures and interfaces. In addition to entire structures and interfaces, the server can assess user-defined subsets. The CAD-score server performs both global and local numerical evaluations of structural differences between structures or interfaces. The results can be explored interactively using sortable tables of global scores, profiles of local errors, superimposed contact maps and 3D structure visualization. The web server could be used for tasks such as comparison of models with the native (reference) structure, comparison of X-ray structures of the same macromolecule obtained in different states (e.g. with and without a bound ligand), analysis of nuclear magnetic resonance (NMR) structural ensemble or structures obtained in the course of molecular dynamics simulation. The web server is freely accessible at: http://www.ibt.lt/bioinformatics/cad-score.

PMID:
24838571
PMCID:
PMC4086110
DOI:
10.1093/nar/gku294
[Indexed for MEDLINE]
Free PMC Article

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