A Merge-Decoupling Dead End Elimination algorithm for protein side-chain conformation.
Dead End Elimination (DEE) is a technique for eliminating rotamers that can not exist in any global minimum energy configuration for the protein side chain conformation problem. A popular method is Simple Goldstein DEE (SG-DEE) which is fast and eliminates rotamers by considering single residues for possible elimination. We present a Merge-Decoupling DEE (MD-DEE) that further reduces the number of rotamers after SG-DEE. MD-DEE works by forming residue-pairs but is fast and, like SG-DEE, is practical even for large proteins. Our experiments show that MD-DEE achieves further reduction in residue elimination (up to 25%) after SG-DEE.
Chong
Ket Fah
KF
Department of Computer Science, National University of Singapore, 3 Science Drive 2, Singapore. chongket@comp.nus.edu.sg
Leong
Hon Wai
HW
D000465:Algorithms; D000595:Amino Acid Sequence; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary