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. 2008;3(7):1171-9.
doi: 10.1038/nprot.2008.91.

Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7

Gerrit Langer  1 , Serge X Cohen, Victor S Lamzin, Anastassis Perrakis
Affiliations

Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7

Gerrit Langer et al. Nat Protoc. 2008.

Abstract

ARP/wARP is a software suite to build macromolecular models in X-ray crystallography electron density maps. Structural genomics initiatives and the study of complex macromolecular assemblies and membrane proteins all rely on advanced methods for 3D structure determination. ARP/wARP meets these needs by providing the tools to obtain a macromolecular model automatically, with a reproducible computational procedure. ARP/wARP 7.0 tackles several tasks: iterative protein model building including a high-level decision-making control module; fast construction of the secondary structure of a protein; building flexible loops in alternate conformations; fully automated placement of ligands, including a choice of the best-fitting ligand from a 'cocktail'; and finding ordered water molecules. All protocols are easy to handle by a nonexpert user through a graphical user interface or a command line. The time required is typically a few minutes although iterative model building may take a few hours.

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Figures

Figure 1
Figure 1
A flowchart of the ARP/wARP procedure. The arrow on top indicates the flow of the data. ARP/wARP modules are labelled in the middle in grey shaded boxes; the numbers in parentheses refer to the steps in Procedure that describe them. The rounded rectangular boxes to the left represent input data (black for required data, light grey for optional input - the sequence - and medium grey for alternative input - the phases or a model) and to the right to the output data. The vertical span of the input / output boxes refers to the procedures they are connected to in the middle.
Figure 2
Figure 2
Trouble shooting for partially ordered ligands. (A) The difference electron density map in the area of the ligand. (B) The ligand adenosylmethionine as modeled in the deposited structure in the PDB (1v2x). (C) A full ligand as built with ARP/wARP. (D) A partial ligand (with the methionine moiety up to its Cβ atom removed) built with ARP/wARP, which matches the density better.
Figure 3
Figure 3
Model completeness achieved by ARP/wARP 7.0 ‘Classic’ as a function of resolution. The blue circles represent a set of diverse structures donated by users in http://xtal.nki.nl/Depot. For these the starting map and the final structure are both known and the model completeness is calculated as the percentage of correct residues compared to the residues in the final structure. The red circles represent a set of diverse structures submitted by users to the ARP/wARP web server (http://cluster.embl-hamburg.de/ARPwARP/remote-http.html). For these structures the starting map or model is known but no final structure is available; thus model completeness is calculated as the percentage of traced residues compared to the anticipated number of residues in the final structure as input by the user. A trend line (counting only the average top 50% of jobs) is also shown for these structures. The lower model completeness even at high resolution for the remotely submitted jobs compared to the Depot structures is likely due to the fact that very rarely all residues in a sequence can ever be built in a crystallographic structure and thus the ARP/wARP performance could be underestimated. We also cannot exclude that many cases that end up in our web server could be the ‘hopeless’ local cases that users attempt to run remotely after failure in their lab.
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References

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