Automated search-model discovery and preparation for structure solution by molecular replacement.

By Ronan M. Keegan, Martyn D. Winn. 2007

144 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology, Computational Chemistry & Drug Discovery

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. A. McCoy
6. G. Bunkoczi
7. T. Croll
8. Nigel W. Moriarty

In Molecular Biology

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

In Computational Chemistry & Drug Discovery

1. Randy J. Read
2. G. Bunkoczi
3. A. McCoy
4. Paul D. Adams
5. R. Oeffner
6. G. Murshudov
7. Yang Zhang
8. Zhidong Xue

Citations in the corpus

• I-TASSER-MR: automated molecular replacement for distant-homology proteins using iterative fragment assembly and progressive sequence truncation (2017, methodology): “MrBUMP used FASTA and/or SSM to pick up templates and then used multiple methods to prepare search models for MR (5,6).”
• Local Error Estimates Dramatically Improve the Utility of Homology Models for Solving Crystal Structures by Molecular Replacement (2015, methodology): “The error estimate for a given model is obtained by calculating the average coordinate error after superimposing the model on all models in the ensemble.”
• 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).”
• Phaser crystallographic software (2007, neutral): “Since then, other major software developments have also started or converted to C++ and Python, for example PyWarp (Cohen et al., 2004), MrBump (Keegan & Winn, 2007) and Pointless (Evans, 2006).”
• The PDB_REDO server for macromolecular structure model optimization (2014, background): “…Winter et al., 2013), 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 &…”
• The Phenix Software for Automated Determination of Macromolecular Structures (2011, methodology): “In fact, with modern computing resources it is not really necessary to choose the model: all plausible models can readily be tested[7, 36].”
• Recent developments in phasing and structure refinement for macromolecular crystallography (2009, methodology): “Molecular replacement pipelines can extend this power even further, by testing alternative strategies for model preparation (CaspR [21] and MrBUMP [22 ]) or building up models using automated databases of domains (BALBES [17 ]).”