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Re‐examination of structure optimization of off‐lattice protein AB models by conformational space annealing
Author(s) -
Lee Jinwoo,
Joo Keehyoung,
Kim SeungYeon,
Lee Jooyoung
Publication year - 2008
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.20995
Subject(s) - lattice (music) , simulated annealing , protein structure prediction , annealing (glass) , crystallography , crystal structure , space (punctuation) , chemistry , computational chemistry , statistical physics , materials science , chemical physics , protein structure , computer science , physics , thermodynamics , algorithm , biochemistry , acoustics , operating system
The global structural optimization is carried out for off‐lattice protein AB models in two and three dimensions by conformational space annealing. The models consist of hydrophobic and hydrophilic monomers in Fibonacci sequences. To accelerate the convergence, we have introduced a shift operator in the internal coordinate system, and effectively reduced the search space by forming a quotient space. With this, we significantly improve our previous results on AB models, and provide new low energy conformations. This work provides insights on exploring complicated energy landscapes by exploiting the advantages and limitations of CSA. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008