Type

Journal Article

Authors

Jens Erik Nielsen
Gianluca Pollastri
Tommy Carstensen
Alison Elizabeth Garrett
Chresten R Søndergaard

Subjects

Biochemistry

Topics
ligands internet reproducibility of results molecular conformation crystallography x ray binding sites chemistry proteins models molecular artifacts metabolism water drug evaluation preclinical

Structural artifacts in protein-ligand X-ray structures: implications for the development of docking scoring functions. (2009)

Abstract The development of docking scoring functions requires high-resolution 3D structures of protein-ligand complexes for which the binding affinity of the ligand has been measured experimentally. Protein-ligand binding affinities are measured in solution experiments, and high resolution protein-ligand structures can be determined only by X-ray crystallography. Protein-ligand scoring functions must therefore reproduce solution binding energies using analyses of proteins in a crystal environment. We present an analysis of the prevalence of crystal-induced artifacts and water-mediated contacts in protein-ligand complexes and demonstrate the effect that these can have on the performance of protein-ligand scoring functions. We find 36% of ligands in the PDBBind 2007 refined data set to be influenced by crystal contacts and find the performance of a scoring function to be affected by these. A Web server for detecting crystal contacts in protein-ligand complexes is available at http://enzyme.ucd.ie/LIGCRYST .
Collections Ireland -> University College Dublin -> PubMed

Full list of authors on original publication

Jens Erik Nielsen, Gianluca Pollastri, Tommy Carstensen, Alison Elizabeth Garrett, Chresten R Søndergaard

Experts in our system

1
Jens Erik Nielsen
University College Dublin
Total Publications: 27
 
2
Gianluca Pollastri
University College Dublin
Total Publications: 35