BALBES: a molecular-replacement pipeline

By F. Long, A. Vagin, P. Young, G. Murshudov. 2007

700 citations recorded by the source corpus.

The fully automated pipeline, BALBES, integrates a redesigned hierarchical database of protein structures with their domains and multimeric organization, and solves molecular-replacement problems using only input X-ray and sequence data.

Subfields: Materials Chemistry, Molecular Biology, 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. Randy J. Read
2. Paul D. Adams
3. Pavel V. Afonine
4. T. C. Terwilliger
5. G. Bunkoczi
6. T. Croll
7. A. McCoy
8. Nigel W. Moriarty

In Molecular Biology

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

In Computational Biology & Bioinformatics

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

Citations in the corpus

• I-TASSER-MR: automated molecular replacement for distant-homology proteins using iterative fragment assembly and progressive sequence truncation (2017, methodology): “BALBES focused on designing a database which was chosen from the PDB with multimeric as well as domain organization (4).”
• Local Error Estimates Dramatically Improve the Utility of Homology Models for Solving Crystal Structures by Molecular Replacement (2015, methodology): “Second, if the correct solution is not found, the resulting LLG value is not valid.”
• Overview of the CCP4 suite and current developments (2011, methodology): “BALBES is based around the MR program MOLREP (Vagin & Teplyakov, 1997, 2010), while MrBUMP can also use the program Phaser (McCoy et al., 2007).”
• Molecular replacement with MOLREP. (2010, methodology): “MOLREP is a component of several MR pipelines, including BALBES (Long et al., 2008), MrBUMP (Keegan & Winn, 2008) and the JCSG pipeline (Schwarzenbacher et al., 2008), that utilize the entire PDB for fully automatic structure determination.”
• Recent developments in phasing and structure refinement for macromolecular crystallography (2009, methodology): “About two-thirds of structures deposited in the PDB are currently solved by molecular replacement, and the proportion could probably be higher [17 ].”
• phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta (2012, methodology): “This result is consistent with the known utility of extensive searches with a variety of molecular replacement templates (e.g., [12, 13].”
• The PDB_REDO server for macromolecular structure model optimization (2014, methodology): “…experimental phasing (e.g. Panjikar et al., 2005; Terwilliger et al., 2009; Pannu et al., 2011), molecular replacement (e.g. Keegan & Winn, 2007; Long et al., 2008; McCoy et al., 2007), density-map tracing and model building (e.g. Perrakis et al., 1999; Ioerger & Sacchettini, 2002; Cowtan,…”
• The Phenix Software for Automated Determination of Macromolecular Structures (2011, methodology): “About two-thirds of structures deposited in the PDB are currently solved by molecular replacement, and the proportion could probably be higher[8].”
• Using iterative fragment assembly and progressive sequence truncation to facilitate phasing and crystal structure determination of distantly related proteins. (2016, methodology): “In addition, automated pipelines such as CaspR (Claude et al., 2004), MrBUMP (Keegan & Winn, 2008) and BALBES (Long et al., 2008) were created to use multiple homologous template search models in order to enhance the success rate of MR.”
• Phaser.MRage: automated molecular replacement (2013, background): “Both BALBES and MrBUMP can decompose homology-search hits into underlying domains.”