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

By G. Langer, Serge X. Cohen, V. Lamzin, Anastassis Perrakis. 2008

1,645 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

Using SAD data in Phaser (2011, positive): “If the map is sufficient to build a partial preliminary model using a program such as ARP/ wARP (Langer et al., 2008), PHENIX AutoBuild (Terwilliger et al., 2008) or Buccaneer (Cowtan, 2006), then this model can be used to re-initiate substructure determination.”
Features and development of Coot (2010, neutral): “In recent years, initial construction of the protein chain has often been carried out using automatic model-building tools such as ARP / wARP (Langer et al. , 2008), SOLVE / RESOLVE (Wang et al. , 2004) and more recently Buccaneer (Cowtan, 2006).”
Overview of the CCP4 suite and current developments (2011, methodology): “A ccp4i interface to the popular ARP/wARP model-building package (Langer et al., 2008) has also been available for many years.”
High‐accuracy protein structure prediction in CASP14 (2021, methodology): “…and a local protein backbone validation score that is used for guiding automated protein model building with ARP/wARP at medium-to-low resolution 20,21 and as a general protein backbone validation score, 22 being also useful for the identification of geometrically strained residues of potentially…”
Ab initio solution of macromolecular crystal structures without direct methods (2017, background): “At this point, the phase information was sufficient to enable phase improvement by density modification in Parrot (18), and the resulting map could be interpreted in terms of an atomic model in ARP/wARP (19).”
phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta (2012, methodology): “Improvements in model-building algorithms include the use of iteration between model-building, reﬁnement and map calculation or density modiﬁcation [17, 18, 19] and the development of methods that can be used at resolutions lower than 3 A˚ [20, 21, 22, 23, 24, 25, 26, 27].”
Structure-based electron-confurcation mechanism of the Ldh-EtfAB complex (2022, methodology): “Maps were visualized with Chimera (Pettersen et al., 2004) and models automatically built with Arp/Warp (Langer et al., 2008) or manually within COOT (Emsley & Cowtan, 2004).”
The pseudokinase MLKL mediates necroptosis via a molecular switch mechanism. (2013, methodology): “Initial building with Arp/Warp (Langer et al., 2008) and refinement with REFMAC5 (Murshudov et al., 2011) provided regions of model and maps sufficient in detail to identify the pseudokinase region.”
Can I solve my structure by SAD phasing? Anomalous signal in SAD phasing (2016, methodology): “…techniques (Wang, 1985; Cowtan & Main, 1996; Abrahams & Leslie, 1996; Terwilliger, 2000; Cowtan, 2010) and interpreted in terms of an atomic model (see, for example, Jones et al., 1991; Perrakis et al., 1999; Emsley et al., 2010; Terwilliger et al., 2008; Cowtan, 2006; Langer et al., 2008).”
Structure of Actin-related protein 8 and its contribution to nucleosome binding (2012, methodology): “An initial model of high quality was obtained using cycles of automated model building with ARP/wARP (27) and BUCCANEER (28) in the CCP4 Suite (29) and completed by manual building using COOT (30).”
AMPLE: a cluster-and-truncate approach to solve the crystal structures of small proteins using rapidly computed ab initio models. (2012, methodology): “…CC > 25% and a mean chain length of >10 residues as successes and verified that all but one case (for which the density indicated partial success) could be automatically rebuilt with ARP/wARP (Langer et al., 2008; Cohen et al., 2008) and/or Buccaneer (Cowtan, 2006) to an Rfree value of below 45%.”
Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum (2012, methodology): “A number of highly automated procedures for model building and model rebuilding have recently been developed (Levitt, 2001; Oldfield, 2002, 2003; Ioerger & Sacchettini, 2003; DePristo et al., 2005; Cowtan, 2006; Langer et al., 2008; Terwilliger et al., 2008).”
MolProbity’s Ultimate Rotamer-Library Distributions for Model Validation (2016, methodology): “9–11,23,43–46 To make model building computationally tractable, the procedure has usually been to initially fit side-chains as discrete conformations at rotamer values, then to minimize or to test at neighboring sample points, using r to inform the allowable range for each v .”
Increasing the Radius of Convergence of Molecular Replacement by Density and Energy Guided Protein Structure Optimization (2011, neutral): “Torsion-space simulated annealing in CNS before autobuilding allowed solution of two additional structures, DEN refinement,threeadditionalstructures,andRosettaenergy-basedstruc-tureoptimization,fourteenadditionalstructures(SupplementaryFig.2 andSupplementaryTables3–5).”
ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps (2018, methodology): “These packages are often capable of building >90% of residues into maps with a resolution of 3 Å or better, with success rates decreasing rapidly beyond this threshold (Terwilliger et al., 2008; Cowtan, 2006; Langer et al., 2008).”
Introduction to phasing (2010, methodology): “The program ARP/wARP is particularly useful and performs cycles of placing dummy atoms into electron-density maps followed by refinement, model building and update (Langer et al., 2008).”