ARP/wARP and molecular replacement.
By Anastassis Perrakis, M. Harkiolaki, K. Wilson, V. Lamzin. Acta Crystallographica Section D: Biological Crystallography, 2001
465 citations recorded by the source corpus.
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.
Subfields: Infectious Diseases, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/cf3b6401c83c5872b6463b5d84df0f6b48edfb77
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In Infectious Diseases
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- Janusz M. Bujnicki
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- Björn Wallner
Citations in the corpus
- Improved Technologies Now Routinely Provide Protein NMR Structures Useful for Molecular Replacement (2011, methodology): “Program ARP/wARP version 7.0 (Perrakis et al., 2001) was used for automatic model building starting from the Phaser MR solution.”
- The utility of comparative models and the local model quality for protein crystal structure determination by Molecular Replacement (2012, methodology): “E. Finally, by using the ARP/wARP program [34], the observed structure factors (experimental structure factors deposited in PDB) and reconstructed phases (theoretical data computed for the REFMAC solution) were used to build the structure of the target protein.”