Re-examination of structure optimization of off-lattice protein AB models by conformational space annealing
✍ Scribed by Jinwoo Lee; Keehyoung Joo; Seung-Yeon Kim; Jooyoung Lee
- Publisher
- John Wiley and Sons
- Year
- 2008
- Tongue
- English
- Weight
- 314 KB
- Volume
- 29
- Category
- Article
- ISSN
- 0192-8651
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✦ Synopsis
Abstract
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