CHAINSAW: a program for mutating pdb files used as templates in molecular replacement

By N. Stein. 2008

572 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

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. T. Croll
3. G. Bunkoczi
4. A. McCoy
5. Martyn D. Winn
6. G. Murshudov
7. Yan Wang
8. Zhidong Xue

In Molecular Biology

1. Randy J. Read
2. T. Croll
3. A. McCoy
4. G. Bunkoczi
5. Martyn D. Winn
6. Yan Wang
7. G. Murshudov
8. Zhidong Xue

Citations in the corpus

• Improvement of molecular-replacement models with Sculptor (2011, methodology): “These algorithms have since been implemented in the CCP4 (Winn et al., 2011) programs CHAINSAW (Stein, 2008) and MOLREP (Vagin & Teplyakov, 2010).”
• Overview of the CCP4 suite and current developments (2011, methodology): “The program CHAINSAW (Stein, 2008) takes as input a sequence alignment which relates residues in the search model to residues in the target protein and uses this information to edit the search model appropriately.”
• Structural basis of WLS/Evi-mediated Wnt transport and secretion (2020, methodology): “To build the WNT8A-WLS model we first made threaded a homology model of WNT8A based on the xWnt8 structure (PDB ID 4F0A) using CHAINSAW (Stein, 2008).”
• 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.”
• Structure-Function Analysis of Heterodimer Formation, Oligomerization, and Receptor Binding of the Staphylococcus aureus Bi-component Toxin LukGH* (2014, methodology): “Chains A and B of Protein Data Bank code 3B07 were processed using Chainsaw (27), and two full octamers were then generated by superimposing them on the 8 dimers in the octameric pores.”
• 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.”
• ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps (2018, methodology): “…built into 3.8 Å resolution cryo-EM density starting from homology models generated from a distantly related archaeal homohexamer using CHAINSAW (Stein, 2008), followed by extensive iterations of manual rebuilding in Coot and refinement with phenix.real_space_refine using Ramachandran and…”