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 Results for DC.creator="A." AND DC.creator="Perrakis" in section 18.8.3 of volume F
Solvent building
Lamzin, V. S., Perrakis, A. and Wilson, K. S.  International Tables for Crystallography (2012). Vol. F, Section 18.8.3.5, pp. 527-528 [ doi:10.1107/97809553602060000862 ]
... the solvent structure is continuously updated. Since ordered solvent in a typical crystal structure comprises about 10% of the model, improvement ...

Building bound ligands
Lamzin, V. S., Perrakis, A. and Wilson, K. S.  International Tables for Crystallography (2012). Vol. F, Section 18.8.3.4, p. 527 [ doi:10.1107/97809553602060000862 ]
... single best model is chosen (Evrard et al., 2007). A technique that compares the shapes of difference-electron-density blobs ... ligand to be built is used to distinguish compounds from a list (cocktail) of ligand candidates. The ligand that fits best ... subsequent restrained refinement. References Evrard, G. X., Langer, G. G., Perrakis, A. & Lamzin, V. S. (2007). Assessment of automatic ...

Building polynucleotide fragments
Lamzin, V. S., Perrakis, A. and Wilson, K. S.  International Tables for Crystallography (2012). Vol. F, Section 18.8.3.3, p. 527 [ doi:10.1107/97809553602060000862 ]
... of nucleic acids in complex with proteins tend to have a less ordered crystalline arrangement, diffract less well and yield structures ... RNA. The problem of polynucleotide chain tracing is formulated in a manner analogous to that for proteins, but instead of peptides ... assembled like those of proteins with the difference that tracing a protein main chain accounts for two conformational degrees of ...

Recognition of secondary structural elements
Lamzin, V. S., Perrakis, A. and Wilson, K. S.  International Tables for Crystallography (2012). Vol. F, Section 18.8.3.2, p. 527 [ doi:10.1107/97809553602060000862 ]
... secondary structural elements 18.8.3.2. Recognition of secondary structural elements At a resolution of 3.0 and worse, where electron-density maps lack atomic features, ARP/wARP uses a different algorithm to build an initial model. Instead of free ... potential C[alpha] atoms on the basis of their density. A statistical pattern-classification approach based on supervised learning is ...

Iterative protein-model building
Lamzin, V. S., Perrakis, A. and Wilson, K. S.  International Tables for Crystallography (2012). Vol. F, Section 18.8.3.1, pp. 526-527 [ doi:10.1107/97809553602060000862 ]
... are used as the main tool for obtaining as full a protein model as possible from the map calculated with the initial phases. A molecular-replacement solution can be directly used as an initial ... work more efficiently, new improved phases can be obtained and a more accurate and complete protein model can be constructed. ...

ARP/wARP applications
Lamzin, V. S., Perrakis, A. and Wilson, K. S.  International Tables for Crystallography (2012). Vol. F, Section 18.8.3, pp. 526-528 [ doi:10.1107/97809553602060000862 ]
... 18.8.3. ARP/wARP applications Although ARP/wARP started life as a tool to build proteins, it now provides a wider spectrum of functionalities. As of the software version 7.1 ... tasks in macromolecular crystallography: (i) iterative protein-model building including a decision-making control module; (ii) fast construction of the ...

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