title: Assessment of automatic ligand building in ARP/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.
authors.affiliation: European Molecular Biology Laboratory (EMBL), c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany. evrard@embl-hamburg.de
authors.forename: Guillaume X
authors.initials: GX
authors.lastname: Evrard
authors.forename: Gerrit G
authors.initials: GG
authors.lastname: Langer
authors.forename: Anastassis
authors.initials: A
authors.lastname: Perrakis
authors.forename: Victor S
authors.initials: VS
authors.lastname: Lamzin
mesh_terms: D000465:Algorithms; D000818:Animals; D001331:Automation; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D006801:Humans; D008024:Ligands; D008958:Models, Molecular; D008968:Molecular Conformation; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012984:Software; D014961:X-Ray Diffraction
chemical_list: D008024:Ligands; D011506:Proteins