A new test set for validating predictions of protein-ligand interaction.
We present a large test set of protein-ligand complexes for the purpose of validating algorithms that rely on the prediction of protein-ligand interactions. The set consists of 305 complexes with protonation states assigned by manual inspection. The following checks have been carried out to identify unsuitable entries in this set: (1) assessing the involvement of crystallographically related protein units in ligand binding; (2) identification of bad clashes between protein side chains and ligand; and (3) assessment of structural errors, and/or inconsistency of ligand placement with crystal structure electron density. In addition, the set has been pruned to assure diversity in terms of protein-ligand structures, and subsets are supplied for different protein-structure resolution ranges. A classification of the set by protein type is available. As an illustration, validation results are shown for GOLD and SuperStar. GOLD is a program that performs flexible protein-ligand docking, and SuperStar is used for the prediction of favorable interaction sites in proteins. The new CCDC/Astex test set is freely available to the scientific community (http://www.ccdc.cam.ac.uk).
Nissink
J Willem M
JW
Cambridge Crystallographic Data Centre, Cambridge, United Kingdom. nissink@ccdc.cam.ac.uk
Murray
Chris
C
Hartshorn
Mike
M
Verdonk
Marcel L
ML
Cole
Jason C
JC
Taylor
Robin
R
D000465:Algorithms; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D018360:Crystallography, X-Ray; D030562:Databases, Protein; D020407:Internet; D008024:Ligands; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000145:classification / Q000378:metabolism*; D015203:Reproducibility of Results; D012107:Research Design; D012984:Software / Q000592:standards; D012997:Solvents; D014867:Water / Q000737:chemistry / Q000378:metabolism
D008024:Ligands; D011506:Proteins; D012997:Solvents; D014867:Water