Building protein backbones from C alpha coordinates.
An automatic procedure for building polyalanine backbones from guiding alpha-carbon positions is presented. Polyalanine backbones are built based on the geometric restraints of angle N-C alpha-C and the knowledge of main-chain dihedral angle distributions. A building module constructs a list of polyalanine backbones that follow exactly the C alpha trace. Then a selection module selects one backbone with the largest portion of phi-psi pairs in favoured regions. Several test cases on C alpha coordinates from X-ray refined structures give acceptable results. Less than 10% of the peptide planes are incorrectly built, and the result is not sensitive to random shift up to 0.5 A of C alpha coordinates.
Luo
Y
Y
Institute of Physical Chemistry, Peking University, Beijing, P.R. China.
Jiang
X
X
Lai
L
L
Qu
C
C
Xu
X
X
Tang
Y
Y
D000595:Amino Acid Sequence; D004798:Enzymes / Q000737:chemistry; D008432:Mathematical Computing; D008958:Models, Molecular; D008969:Molecular Sequence Data; D015394:Molecular Structure; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012984:Software
D004798:Enzymes; D010455:Peptides; D011506:Proteins; C019529:polyalanine