AMPLE: a cluster-and-truncate approach to solve the crystal structures of small proteins using rapidly computed ab initio models.

By Jaclyn Bibby, Ronan M. Keegan, O. Mayans, Martyn D. Winn, Daniel J. Rigden. 2012

98 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology, Spectroscopy

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. G. Bunkoczi
5. Yan Wang
6. A. McCoy
7. R. Oeffner
8. Zhidong Xue

In Molecular Biology

1. Randy J. Read
2. Paul D. Adams
3. G. Bunkoczi
4. Pavel V. Afonine
5. Yan Wang
6. Yang Zhang
7. A. McCoy
8. Zhidong Xue

In Spectroscopy

1. A. McCoy
2. R. Oeffner
3. Zhidong Xue
4. Jouko Virtanen
5. Yan Wang
6. Paul D. Adams
7. G. Bunkoczi
8. Randy J. Read

Citations in the corpus

• I-TASSER-MR: automated molecular replacement for distant-homology proteins using iterative fragment assembly and progressive sequence truncation (2017, background): “els to solve the crystal structures of small proteins based on a cluster-and-truncate approach (10).”
• High‐accuracy protein structure prediction in CASP14 (2021, methodology): “The modifications made to AMPLE are now available through CCP4.”
• Using iterative fragment assembly and progressive sequence truncation to facilitate phasing and crystal structure determination of distantly related proteins. (2016, methodology): “Following Bibby et al. (2012), as well as our observation of a strong correlation between modeling accuracy and structural diversity of I-TASSER simulations (Zhang, 2008a; Zhang et al., 2003), we defined an average variation score (AVS) for the ith residue as AVSi ¼ 1 M PM j¼1 ½ðxj;i xC;iÞ 2 þ…”
• Phaser.MRage: automated molecular replacement (2013, methodology): “…in automatic model building, especially the integration of structure modelling in, for example, phenix.mr_rosetta (DiMaio et al., 2011) and AMPLE (Bibby et al., 2012), have increased the radius of convergence for refinement and led to successful structure determination from borderline…”
• On the application of the expected log-likelihood gain to decision making in molecular replacement (2018, background): “…has focused on the generation of more general structural fragments, including those from distant homologues (ARCIMBOLDO_SHREDDER; Sammito et al., 2014; Millán et al., 2018), libraries of structural motifs (ARCIMBOLDO_BORGES; Sammito et al., 2013) or molecular modelling (AMPLE; Bibby et al., 2012).”