TY  - JOUR
AU  - Strodel, B.
AU  - Bauer, M.S.
AU  - Fejer, S.N.
AU  - Koslover, E.F.
AU  - Wales, D.J.
TI  - Interpolation Schemes for Peptide Rearrangements
JO  - The journal of chemical physics
VL  - 132
SN  - 0021-9606
CY  - Melville, NY
PB  - American Institute of Physics
M1  - PreJuSER-9867
SP  - 054101
PY  - 2010
N1  - M.B. gratefully acknowledges the Gates Cambridge Trust for financial support.
AB  - 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.
KW  - Algorithms
KW  - Artificial Intelligence
KW  - Computer Simulation
KW  - Image Enhancement
KW  - Image Interpretation, Computer-Assisted
KW  - Mathematics: methods
KW  - Molecular Sequence Data
KW  - Pattern Recognition, Automated
KW  - Peptides: chemistry
KW  - Protein Conformation
KW  - Protein Folding
KW  - Thermodynamics
KW  - Peptides (NLM Chemicals)
KW  - J (WoSType)
LB  - PUB:(DE-HGF)16
C6  - pmid:20136299
UR  - <Go to ISI:>//WOS:000274319900002
DO  - DOI:10.1063/1.3273617
UR  - https://juser.fz-juelich.de/record/9867
ER  -