Interpolation schemes for peptide rearrangements.
A variety of methods (in total seven) comprising different combinations of internal and Cartesian coordinates are tested for interpolation and alignment in connection attempts for polypeptide rearrangements. We consider Cartesian coordinates, the internal coordinates used in CHARMM, and natural internal coordinates, each of which has been interfaced to the OPTIM code and compared with the corresponding results for united-atom force fields. We show that aligning the methylene hydrogens to preserve the sign of a local dihedral angle, rather than minimizing a distance metric, provides significant improvements with respect to connection times and failures. We also demonstrate the superiority of natural coordinate methods in conjunction with internal alignment. Checking the potential energy of the interpolated structures can act as a criterion for the choice of the interpolation coordinate system, which reduces failures and connection times significantly.
Bauer
Marianne S
MS
University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, United Kingdom.
Strodel
Birgit
B
Fejer
Szilard N
SN
Koslover
Elena F
EF
Wales
David J
DJ
D000465:Algorithms; D001185:Artificial Intelligence; D003198:Computer Simulation; D007089:Image Enhancement; D007090:Image Interpretation, Computer-Assisted; D008433:Mathematics / Q000379:methods; D008969:Molecular Sequence Data; D010363:Pattern Recognition, Automated; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D017510:Protein Folding; D013816:Thermodynamics
D010455:Peptides