Automated ligand fitting by core-fragment fitting and extensioninto density
A procedure for fitting of ligands to electron- density mapsby first fitting a core fragment of the ligand to density and thenextending the remainder of the ligand into density is presented. Theapproach was tested by fitting 9327 ligands over a wide range ofresolutions ( most are in the range 0.8-4.8 angstrom) from the ProteinData Bank (PDB) into (F-o - F-c) exp(i phi(c)) difference densitycalculated using entries from the PDB without these ligands. Theprocedure was able to place 58 percent of these 9327 ligands within 2angstrom (r.m. s.d.) of the coordinates of the atoms in the original PDBentry for that ligand. The success of the fitting procedure wasrelatively insensitive to the size of the ligand in the range 10 -100non-H atoms and was only moderately sensitive to resolution, with thepercentage of ligands placed near the coordinates of the original PDBentry for fits in the range 58 - 73 percent over all resolution rangestested.
- Research Organization:
- COLLABORATION - Los Alamos NatlLab
- DOE Contract Number:
- DE-AC02-05CH11231
- OSTI ID:
- 928590
- Report Number(s):
- LBNL-62893; TRN: US200811%%415
- Journal Information:
- ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICALCRYSTALLOGRAPHY, Vol. 62, Issue 8; Related Information: Journal Publication Date: Aug 2006
- Country of Publication:
- United States
- Language:
- English
Similar Records
Automated ligand fitting by core-fragment fitting and extension into density
Ligand identification using electron-density mapcorrelations