ARP/wARP and molecular replacement.
The aim of ARP/wARP is improved automation of model building and refinement in macromolecular crystallography. Once a molecular-replacement solution has been obtained, it is often tedious to refine and rebuild the initial (search) model. ARP/wARP offers three options to automate that task to varying extents: (i) autobuilding of a completely new model based on phases calculated from the molecular-replacement solution, (ii) updating of the initial model by atom addition and deletion to obtain an improved map and (iii) docking of a structure onto a new (or mutated) sequence, followed by rebuilding and refining the side chains in real space. A few examples are presented where ARP/wARP made a considerable difference in the speed of structure solution and/or made possible refinement of otherwise difficult or uninterpretable maps. The resolution range allowing complete autobuilding of protein structures is currently 2.0 A, but for map improvement considerable advances over more conventional refinement techniques are evident even at 3.2 A spacing.
Perrakis
A
A
Department of Molecular Carcinogenesis, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands. perrakis@nki.nl
Harkiolaki
M
M
Wilson
K S
KS
Lamzin
V S
VS
D020087:Alu Elements; D017089:Ankyrin Repeat; D000081242:B-Cell Lymphoma 3 Protein; D001412:Bacillus subtilis / Q000737:chemistry; D001425:Bacterial Outer Membrane Proteins; D001426:Bacterial Proteins / Q000737:chemistry; D018360:Crystallography, X-Ray; D004860:Infectious Anemia Virus, Equine / Q000737:chemistry; D033862:Iron-Binding Proteins; D008958:Models, Molecular; D033902:Periplasmic Binding Proteins; D011506:Proteins / Q000737:chemistry*; D011518:Proto-Oncogene Proteins / Q000737:chemistry; D011755:Pyrophosphatases / Q000737:chemistry; D016601:RNA-Binding Proteins / Q000737:chemistry; D018271:Signal Recognition Particle / Q000737:chemistry; D012984:Software; D014157:Transcription Factors
D000081242:B-Cell Lymphoma 3 Protein; D001425:Bacterial Outer Membrane Proteins; D001426:Bacterial Proteins; D033862:Iron-Binding Proteins; D033902:Periplasmic Binding Proteins; D011506:Proteins; D011518:Proto-Oncogene Proteins; D016601:RNA-Binding Proteins; D018271:Signal Recognition Particle; D014157:Transcription Factors; D011755:Pyrophosphatases; C020020:dUTP pyrophosphatase