Assessment of automatic ligand building inARP/wARP

Abstract

The efficiency of the ligand-building module of ARP/wARP version 6.1 has been assessed through extensive tests on a large variety of protein-ligand complexes from the PDB, as available from the Uppsala Electron Density Server. Ligand building in ARP/wARP involves two main steps: automatic identification of the location of the ligand and the actual construction of its atomic model. The first step is most successful for large ligands. The second step, ligand construction, is more powerful with X-ray data at high resolution and ligands of small to medium size. Both steps are successful for ligands with low to moderate atomic displacement parameters. The results highlight the strengths and weaknesses of both the method of ligand building and the large-scale validation procedure and help to identify means of further improvement.

Crystal Structure and Computational Characterization of the Lytic Polysaccharide Monooxygenase GH61D from the Basidiomycota Fungus Phanerochaete chrysosporium

“…For cross-validation and R and R free calculations, 5% of the data was excluded from the structure refinement (39). Solvent molecules were automatically added using the automatic water picking function in the ARP/wARP package (40). Picked water molecules were selected or discarded manually by visual inspection of the 2F o Ϫ F c electron density map.…”

Perturbation of the Quinone-binding Site of Complex II Alters the Electronic Properties of the Proximal [3Fe-4S] Iron-Sulfur Cluster

“…Ideal coordinates for the malate-like intermediate TEO were obtained from the HIC-Up data base (26) and input to the PRODRG server to generate final coordinate and restraint files for modeling. The ligand building procedure within ARP/ wARP (27) was used to fit carboxin into the density map. Water molecules were fitted using phenix.refine and Coot and validated using Coot.…”

Insights Into the Enzymatic Mechanism of 6-Phosphogluconolactonase from Trypanosoma brucei Using Structural Data and Molecular Dynamics Simulation

“…17 Water molecules wwere added by the standard procedure with the ARP/warp suite. 18 The stereochemical quality of the refined models was assessed using the program Procheck. 19 Refinement statistics for both complexes are given in Table 2.…”