Spherically averaged phased translation function and its application to the search for molecules and fragments in electron-density maps.

By A. Vagin, M. Isupov. 2001

224 citations recorded by the source corpus.

The molecular-replacement method has been extended to locate molecules and their fragments in an electron-density map. The approach is based on a new spherically averaged phased translation function. The position of the centre of mass of a search model is found prior to determination of its orientation. The orientation is subsequently found by a phased rotation function. The technique also allows superposition of distantly related macromolecules. The method has been implemented in a computer program MOLREP and successfully tested using experimental data sets.

Subfields: Computational Theory and Mathematics, 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 Computational Theory and Mathematics

1. A. Teplyakov
2. Martyn D. Winn
3. Tom Burnley
4. Colin M. Palmer
5. Daniel J. Rigden
6. Rhiju Das
7. Thomas Mulvaney
8. Rachael Kretsch

In Materials Chemistry

1. Daniel J. Rigden
2. Martyn D. Winn
3. Andriy Kryshtafovych
4. Maya Topf
5. Tom Burnley
6. Rhiju Das
7. Colin M. Palmer
8. A. Teplyakov

In Molecular Biology

1. Martyn D. Winn
2. Daniel J. Rigden
3. Tom Burnley
4. Andriy Kryshtafovych
5. Colin M. Palmer
6. A. Teplyakov
7. Maya Topf
8. Rhiju Das

Citations in the corpus

• GC1118, an Anti-EGFR Antibody with a Distinct Binding Epitope and Superior Inhibitory Activity against High-Affinity EGFR Ligands (2015, methodology): “The sEGFR–GC1118 complex structure was determined by themolecular replacementmethodwithMolrep in CCP4 suite using the sEGFR structure and Fab structure, respectively, from sEGFR–cetuximab complex structure (PDB ID: 1YY9) as a search model (28, 29).”
• Regulation of the transcriptional activator NtrC1: structural studies of the regulatory and AAA+ ATPase domains. (2003, methodology): “Seven two-fold NCS peaks were found (at about 5s) using the selfrotation function of Molrep (Vagin and Isupov 2001).”
• CASP15 cryoEM protein and RNA targets: refinement and analysis using experimental maps (2023, methodology): “Molrep incorporates a Spherically Averaged Phased Translation Function (SAPTF), followed by a Rotation Function (RF) and Phased Translation Function (PTF), which achieves a suggested first fit and then improves the overlap score with a six-dimensional optimisation search 9,10 .”
• Recent developments in the CCP-EM software suite (2017, methodology): “A spherically averaged phased translation function can also be used in which the centre of mass of the input model is found before optimizing the orientation (Vagin & Isupov, 2001), which can be advantageous when using distantly related search models or with lower resolution maps.”
• Molecular replacement with MOLREP. (2010, methodology): “(i) The model is positioned in the cell using the spherically averaged TF (Vagin & Isupov, 2001).”
• CASP15 cryo-EM protein and RNA targets: refinement and analysis using experimental maps (2023, methodology): “The docking of models in this study was carried out using two automatic docking programs, Molrep 10,11 and PowerFit.”