Visualizing ligand molecules in Twilight electron density.
Acta Crystallogr Sect F Struct Biol Cryst Commun
; 69(Pt 2): 195-200, 2013 Feb 01.
Article
em En
| MEDLINE
| ID: mdl-23385767
ABSTRACT
Three-dimensional models of protein structures determined by X-ray crystallography are based on the interpretation of experimentally derived electron-density maps. The real-space correlation coefficient (RSCC) provides an easily comprehensible, objective measure of the residue-based fit of atom coordinates to electron density. Among protein structure models, protein-ligand complexes are of special interest, given their contribution to understanding the molecular underpinnings of biological activity and to drug design. For consumers of such models, it is not trivial to determine the degree to which ligand-structure modelling is biased by subjective electron-density interpretation. A standalone script, Twilight, is presented for the analysis, visualization and annotation of a pre-filtered set of 2815 protein-ligand complexes deposited with the PDB as of 15 January 2012 with ligand RSCC values that are below a threshold of 0.6. It also provides simplified access to the visualization of any protein-ligand complex available from the PDB and annotated by the Uppsala Electron Density Server. The script runs on various platforms and is available for download at http//www.ruppweb.org/twilight/.
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Base de dados:
MEDLINE
Assunto principal:
Software
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Limite:
Humans
Idioma:
En
Ano de publicação:
2013
Tipo de documento:
Article