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

@article{citeulike:5659650, 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 .}, author = {S{\o}ndergaard, Chresten R. and Garrett, Alison Elizabeth E. and Carstensen, Tommy and Pollastri, Gianluca and Nielsen, Jens Erik E.}, citeulike-article-id = {5659650}, citeulike-linkout-0 = {http://www.biomedexperts.com/Abstract.bme/19711919}, citeulike-linkout-1 = {http://dx.doi.org/10.1021/jm8016464}, citeulike-linkout-2 = {http://pubs.acs.org/doi/abs/10.1021/jm8016464}, citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/19711919}, citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=19711919}, day = {24}, doi = {10.1021/jm8016464}, issn = {1520-4804}, journal = {Journal of medicinal chemistry}, keywords = {crystallography, pdbbind}, month = {September}, number = {18}, pages = {5673--5684}, posted-at = {2009-09-01 20:50:40}, priority = {2}, title = {Structural artifacts in protein-ligand X-ray structures: implications for the development of docking scoring functions.}, url = {http://dx.doi.org/10.1021/jm8016464}, volume = {52}, year = {2009} }

TY - JOUR ID - citeulike:5659650 L3 - citeulike-article-id:5659650 N2 - 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 . IS - 18 JF - Journal of medicinal chemistry SN - 1520-4804 EP - 5684 TI - Structural artifacts in protein-ligand X-ray structures: implications for the development of docking scoring functions. VL - 52 SP - 5673 KW - crystallography KW - pdbbind AU - Søndergaard, Chresten AU - Garrett, Alison Elizabeth AU - Carstensen, Tommy AU - Pollastri, Gianluca AU - Nielsen, Jens Erik PY - 2009/09/24/ UR - http://dx.doi.org/10.1021/jm8016464 ER -