Improvement of molecular-replacement models with Sculptor

By G. Bunkoczi, Randy J. Read. 2011

204 citations recorded by the source corpus.

The molecular-replacement model-improvement program Sculptor is described, with an analysis of the algorithms used.

Subfields: Materials Chemistry, Molecular Biology, Spectroscopy, 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. Paul D. Adams
2. Pavel V. Afonine
3. Randy J. Read
4. T. C. Terwilliger
5. Nigel W. Moriarty
6. T. Croll
7. Yang Zhang
8. David Baker

In Molecular Biology

1. Paul D. Adams
2. Randy J. Read
3. Pavel V. Afonine
4. T. C. Terwilliger
5. Yang Zhang
6. David Baker
7. Andriy Kryshtafovych
8. Nigel W. Moriarty

In Spectroscopy

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

In Computational Chemistry & Drug Discovery

1. Randy J. Read
2. A. McCoy
3. G. Bunkoczi
4. R. Oeffner
5. David Baker
6. Paul D. Adams
7. T. Croll
8. Nathaniel Echols

Citations in the corpus

• Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix (2019, methodology): “The search model can be enhanced by trimming off parts of the model that are unlikely to be preserved in the target structure using Sculptor (phenix.sculptor; Bunkóczi & Read, 2011).”
• I-TASSER-MR: automated molecular replacement for distant-homology proteins using iterative fragment assembly and progressive sequence truncation (2017, methodology): “Results showed that I-TASSER-MR found correct MR solutions for 95 out of the 161 targets as judged by having a translation function Z-score (TFZ) of >8 or as having the final structure be closer to the native than the initial search models; this number is 36% higher than that obtained by the CHAINSA”
• Local Error Estimates Dramatically Improve the Utility of Homology Models for Solving Crystal Structures by Molecular Replacement (2015, methodology): “The local errors of these models were predicted by ProQ2 (Ray et al., 2012), converted into B factors, then mapped onto the corresponding MR model, which was generated from the same template and the same alignment using Sculptor (Bunko´czi and Read, 2011).”
• Evaluation of template-based modeling in CASP13 (2019, methodology): “Models, pruned first to match the evaluation units, were prepared using the program Sculptor, 35 which prunes atoms from loops and side chains that the sequence alignment implies are unlikely to be present in the target.”
• Phaser.MRage: automated molecular replacement (2013, methodology): “The only exception seems to be models sharing the same template (generated using different Sculptor protocols), which can be scored without refinement.”
• Improved estimates of coordinate error for molecular replacement (2013, methodology): “The structures corresponding to these PDB entries were pruned and edited with Sculptor (Bunkóczi & Read, 2011) using the default protocol.”
• On the application of the expected log-likelihood gain to decision making in molecular replacement (2018, methodology): “A model was prepared from PDB entry 2d71 using Sculptor (Bunkóczi & Read, 2011).”
• 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).”
• The Phenix Software for Automated Determination of Macromolecular Structures (2011, methodology): “Both model trimming and B-factor weighting are available in the Sculptor tool in Phenix[38].”
• phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta (2012, background): “Improved 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…”
• Using iterative fragment assembly and progressive sequence truncation to facilitate phasing and crystal structure determination of distantly related proteins. (2016, methodology): “The first successful I-TASSER search model has an r.m.s.d. of 1.76 Å and a TM-score of 0.69, while the r.m.s.d. and TM-score of the best of 13 LOMETS search models produced by CHAINSAW and Sculptor are 2.0 Å and 0.62, respectively.”