The JCSG MR pipeline: optimized alignments, multiple models and parallel searches

By R. Schwarzenbacher, Adam Godzik, Lukasz Jaroszewski. 2007

29 citations recorded by the source corpus.

The practical limits of molecular replacement can be extended by using several specifically designed protein models based on fold-recognition methods and by exhaustive searches performed in a parallelized pipeline. Updated results from the JCSG MR pipeline, which to date has solved 33 molecular-replacement structures with less than 35% sequence identity to the closest homologue of known structure, are presented.

Subfields: Materials Chemistry, Molecular Biology

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

In Materials Chemistry

1. Yang Zhang
2. Torsten Schwede
3. Yan Wang
4. Zhidong Xue
5. Jouko Virtanen
6. A. Teplyakov
7. J. Haas
8. A. Vagin

In Molecular Biology

1. Yang Zhang
2. Torsten Schwede
3. Yan Wang
4. Zhidong Xue
5. Jouko Virtanen
6. Björn Wallner
7. A. Teplyakov
8. J. Haas

Citations in the corpus

• I-TASSER-MR: automated molecular replacement for distant-homology proteins using iterative fragment assembly and progressive sequence truncation (2017, methodology): “designed the JCSG MR pipeline according to their finding that the more sophisticated profile–profile alignment methods (FFAS) can improve distant-homology template detection and increase the success rate of MR in cases of low target-template similarity (8,9).”
• BALBES: a molecular-replacement pipeline (2007, methodology): “Nevertheless, several automated molecular-replacement pipelines have already been made available to the user community, including NORMA (Delarue, 2008), MrBUMP (Keegan & Winn, 2008) and part of the JSCS structure-solution pipeline (Schwarzenbacher et al., 2008).”
• Assessment of template based protein structure predictions in CASP9 (2011, background): “2–6 However, many applications require atomic models of high resolution, for example, for designing and interpreting amino acid mutations or studying molecular mechanisms such as ligand binding, transport phenomena, or catalytic processes.”
• 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.”
• The utility of comparative models and the local model quality for protein crystal structure determination by Molecular Replacement (2012, background): “We decided to do that because insertions are more likely to contain significant errors, and if they are not removed, the errors may cause a model to fail in MR [8,39].”