Implementation of molecular replacement in AMoRe.

By J. Navaza. 2001

613 citations recorded by the source corpus.

An account is given of the molecular replacement method as implemented in the package AMoRe. The overall strategy of the method is presented and the main functions used in the package are described. The most important features of AMoRe are the quality of the fast rotation and translation functions and the facility of multiple inputs to translation and rigid-body refinement functions, which allow for a fast multiple exploration of crystal configurations with a high level of automation.

Subfields: Materials Chemistry, Physical and Theoretical Chemistry

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In Materials Chemistry

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Citations in the corpus

Structure of bovine rhodopsin in a trigonal crystal form. (2003, background): “The main chain is coloured in the four segments that project above the lipid phosphate groups and form the cytoplasmic domain: C1 loop region (residues 64-71), C2 loop region (134-152), C3 loop region (225-252), and H8 and C-terminal tail (310-326).”
Improved Technologies Now Routinely Provide Protein NMR Structures Useful for Molecular Replacement (2011, methodology): “Armed with more accurate target functions, more advanced mathematical models and more effective search strategies, a number of software packages have been developed which have greatly improved the effectiveness of the MR approach, such as COMO (Jogl et al., 2001), XPLOR/CNS (Brunger et al., 1998), A”
Spherical polar Fourier assembly of protein complexes with arbitrary point group symmetry (2016, background): “…to be able to generate high-quality candidate complex structures for use as templates in molecular replacement (MR) techniques (Rossmann, 1990; Navaza, 2001), to provide angular parameters for locked MR search functions (Tong, 2001) or to dock high-resolution structural models into…”
Structure of the dengue virus envelope protein after membrane fusion (2004, methodology): “Domain II was placed first, followed by domain I, with AmoR”
Molecular replacement with MOLREP. (2010, methodology): “These include AMoRe (Navaza, 2001), Phaser (McCoy et al., 2007) and the MR implementation in CNS (Brünger et al., 1998).”
CaspR: a web server for automated molecular replacement using homology modelling (2004, methodology): “These models are automatically screened in search of a molecular replacement solution using the AMoRe software ( 9 ).”
Structure of HoxA9 and Pbx1 bound to DNA: Hox hexapeptide and DNA recognition anterior to posterior. (2003, methodology): “The structure was solved by molecular replacement with AMoRe (Navaza 2001), using as a search model the HoxB1/Pbx1/DNA structure (PDB code 1B72) with the HoxB1 hexapeptide deleted (Piper et al. 1999).”
Structural basis for specific binding of Polycomb chromodomain to histone H3 methylated at Lys 27. (2003, methodology): “Figures were prepared using PyMol (DeLano 2002), Molscript (Kraulis 1991), Raster3D (Merritt and Bacon 1997), and Grasp (Nicholls et al. 1991).”