The importance of alignment accuracy for molecular replacement.

By R. Schwarzenbacher, Adam Godzik, Slawomir K. Grzechnik, Lukasz Jaroszewski. 2004

152 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

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In Materials Chemistry

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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).”
Improvement of molecular-replacement models with Sculptor (2011, methodology): “It has been established by Schwarzenbacher et al. (2004) that a correct alignment is very important for optimal modification.”
Phaser crystallographic software (2007, methodology): “There are also various ways of editing structures before use as MR models (Schwarzenbacher et al., 2004).”
Assessment of CASP7 predictions in the high accuracy template‐based modeling category (2007, background): “9 However, there have been signs that modeling algorithms have improved to the point that they can now be useful for molecular replacement.”
Phaser.MRage: automated molecular replacement (2013, background): “…improvements in the accuracy of homology detection (Jaroszewski et al., 2005; Söding et al., 2005) and developments in model improvement (Schwarzenbacher et al., 2004; Bunkóczi & Read, 2011) have enabled the reliable identification of more distant homologues and improved their…”
High resolution protein structure prediction and the crystallographic phase problem (2007, background): “from the NMR structure ensemble; (3) preparation of blind predictions; (4)”
The Phenix Software for Automated Determination of Macromolecular Structures (2011, methodology): “The best strategy was to use sensitive profile-profile alignment techniques to determine which parts of the template would not be preserved, and then to trim off loops and sidechains[37].”
Structures of bovine, equine and leporine serum albumin. (2012, methodology): “The amino-acid sequence was modified with the program CHAINSAW (Stein, 2008; Schwarzenbacher et al., 2004); the side chains were removed from the model, leaving only the part common to the sequence of the target protein.”
Comparative Protein Structure Modeling Using MODELLER (2016, methodology): “Models with such high accuracy have been shown to be useful even for refining crystallographic structures by the method of molecular replacement (Howell et al., 1992; Baker and Sali, 2001; Jones, 2001; Claude et al., 2004; Schwarzenbacher et al., 2004).”
phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta (2012, methodology): “…starting templates for molecular replacement have been obtained by judicious pruning of parts of models that are less likely to be correct [5, 6, 7], by creating ensembles of templates [8, 9], using normal mode analysis [10, 11], and by systematic searches using many or all of the proteins in…”
On the application of the expected log-likelihood gain to decision making in molecular replacement (2018, methodology): “…the Protein Data Bank prior to molecular replacement is a well established method for improving the signal, and often makes the difference between success and failure (Schwarzenbacher et al., 2004; Bunkóczi & 250 Oeffner et al. Expected LLG in decision making in molecular replacement Acta Cryst.”
FFAS03: a server for profile–profile sequence alignments (2005, methodology): “Molecular replacement search models based on the FFAS alignments allowed determination of several protein structures impossible to solve with less accurate models (30).”
Comparative Protein Structure Modeling Using Modeller (2006, methodology): “Models with such high accuracy have been shown to be useful even for refining crystallographic structures by the method of molecular replacement (Howell et al., 1992; Baker and Sali, 2001; Jones, 2001; Claude et al., 2004; Schwarzenbacher et al., 2004).”
The utility of comparative models and the local model quality for protein crystal structure determination by Molecular Replacement (2012, methodology): “Finally, as shown by the Godzik group [8], the likelihood of solving the phase problem for a given protein increases for extensive MR searches using the population of alternative alignments.”
MUSTANG: A multiple structural alignment algorithm (2006, background): “This is crucial for solving difficult MR problems where the sequence identity of available MR probes is low.(3) In addition, high-quality multiple alignments, based on structures, will improve the sensitivity of iterative database searching procedures such as PSI-BLAST.”
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): “The success of molecular replacement depends on optimal sequence alignment between homologous structure and target sequence (Schwarzenbacher et al., 2004; Bunkóczi & Read, 2011).”