Methodology and applications of automatic electron-density map interpretation by six-dimensional rotational and translational search for molecular fragments.
The electron density for a search fragment and for the crystal is expanded in the space of spherical harmonics Bessel functions. The fast rotation function is evaluated for each grid point to test if the fragment can be orientated there. For the best scoring points, the six-dimensional coordinates of the fragment are refined by the second-derivative block-diagonal procedure. The method is able to locate fragments precisely over a wide range of resolutions for structure types from small organic molecules to proteins.
Pavelcik
Frantisek
F
The University of Texas, Southwestern Medical Center at Dallas, Department of Biochemistry, 5323 Harry Hines Boulevard, Dallas, Texas 75235, USA. pavelcik@fns.uniba.sk
Zelinka
Jan
J
Otwinowski
Zbyszek
Z
D001426:Bacterial Proteins; D001643:Bridged Bicyclo Compounds / Q000737:chemistry; D020916:Conotoxins / Q000737:chemistry; D004583:Electrons; D007091:Image Processing, Computer-Assisted; D008958:Models, Molecular; D010446:Peptide Fragments / Q000737:chemistry; D010456:Peptides, Cyclic / Q000737:chemistry; D010940:Plant Proteins / Q000737:chemistry; D014176:Protein Biosynthesis; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D011897:Random Allocation; D012808:Sigma Factor / Q000737:chemistry
D001426:Bacterial Proteins; D001643:Bridged Bicyclo Compounds; D020916:Conotoxins; D010446:Peptide Fragments; D010456:Peptides, Cyclic; D010940:Plant Proteins; D011506:Proteins; C422477:SigI protein, Bacillus subtilis; D012808:Sigma Factor; C455286:cyclo(Gly-Pro-Pro-Gly-Pro-Pro); C024934:crambin protein, Crambe abyssinica