The Buccaneer software for automated model building. 1. Tracing protein chains.

By Kevin Cowtan. 2006

1,816 citations recorded by the source corpus.

A new technique for the automated tracing of protein chains in experimental electron-density maps is described. The technique relies on the repeated application of an oriented electron-density likelihood target function to identify likely C(alpha) positions. This function is applied both in the location of a few promising ;seed' positions in the map and to grow those initial C(alpha) positions into extended chain fragments. Techniques for assembling the chain fragments into an initial chain trace are discussed.

Subfields: Materials Chemistry, Molecular Biology, Spectroscopy, Computational Biology & Bioinformatics

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Materials Chemistry

1. Paul D. Adams
2. Randy J. Read
3. Pavel V. Afonine
4. T. Croll
5. T. C. Terwilliger
6. G. Murshudov
7. A. McCoy
8. Nigel W. Moriarty

In Molecular Biology

1. Randy J. Read
2. Paul D. Adams
3. T. Croll
4. T. C. Terwilliger
5. Pavel V. Afonine
6. A. McCoy
7. G. Murshudov
8. G. Bunkoczi

In Spectroscopy

1. Randy J. Read
2. Paul D. Adams
3. A. McCoy
4. G. Bunkoczi
5. T. C. Terwilliger
6. T. Croll
7. G. Murshudov
8. Tom Burnley

In Computational Biology & Bioinformatics

1. Randy J. Read
2. Paul D. Adams
3. Pavel V. Afonine
4. T. Croll
5. A. McCoy
6. G. Murshudov
7. G. Bunkoczi
8. Martyn D. Winn

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).”
• Protein sequence design with a learned potential (2022, methodology): “The high-resolution F2C structure was traced with Buccaneer 73 and went through manual fi tting using COOT 74 and re fi nement using REFMAC 75 .”
• Overview of the CCP4 suite and current developments (2011, methodology): “The CCP4 suite includes an interface for alternating cycles of model building with Buccaneer with cycles of model refinement with REFMAC5.”
• DIALS: implementation and evaluation of a new integration package (2018, methodology): “Density-modified phases were used for automated model building with Buccaneer (Cowtan, 2006) and a single molecule per asymmetric unit was built, resulting in an initial Rwork of 26.36% and Rfree of 28.37% before further refinement.”
• Immunogenicity and structures of a rationally designed prefusion MERS-CoV spike antigen (2017, methodology): “This model was then used as input for Buccaneer (82), which produced a model containing all 341 residues.”
• Structural insights into the assembly of the histone deacetylase-associated Sin3L/Rpd3L corepressor complex (2015, methodology): “After solvent flattening by AutoSHARP (55), a nearly complete initial model was generated using Buccaneer (56) in CCP4 (57).”
• 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).”
• Constructing and Validating Initial Cα Models from Subnanometer Resolution Density Maps with Pathwalking (2012, background): “X-ray crystallographic tools exist for (semi-) automatic model building, however these utilities are targeted to higher resolution density maps, though some can potentially be applied to 3–4 Å resolution density maps (Cohen et al., 2004; Cowtan, 2006).”
• 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 a phleboviral envelope glycoprotein reveals a consolidated model of membrane fusion (2016, methodology): “Initial phases were obtained using the SAD method in autoSHARP (51), and Buccaneer, as implemented in autoSHARP, was used for initial model building (52).”
• Recent developments in classical density modification (2010, methodology): “To this end, automated model-building calculations were performed using the Buccaneer modelbuilding software (Cowtan, 2006) starting from the modified phases from each density-modification program in turn.”
• Crystal structure determination and refinement via SIR2014 (2015, methodology): “An automated model building (AMB) program [i.e. ARP/wARP (Perrakis et al., 1999; Langer et al., 2008), Buccaneer (Cowtan, 2006, 2008), Nautilus (Cowtan, 2012), a specific tool for nucleic acid model building, or PHENIX Autobuild (Terwilliger et al., 2008; Adams et al., 2010)] may be applied, to chec”