A simplified homology-model builder toward highly protein-like structures: An inspection of restraining potentials

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Title
A simplified homology-model builder toward highly protein-like structures: An inspection of restraining potentials
Author(s)
T R Kim; Sangho Oh; Joshua Sungwoo Yang; Sanghyuk Lee; S Shin; Jinhyuk Lee
Bibliographic Citation
Journal of Computational Chemistry, vol. 33, no. 24, pp. 1927-1935
Publication Year
2012
Abstract
A homology model builder using simple restraining potentials based on spline-interpolated quadratic functions is developed and interfaced with CHARMM package. The continuity and stability of the potential function were validated, and the parameters were optimized using the CASP7 targets. The performance of the model builder was benchmarked to the Modeller program using the template-based modeling targets in CASP9. The benchmark results show that, while our builder yields the structures with slightly lower packing, backbone, and template modeling scores, our models show much better protein-like scores in terms of normalized discrete optimized protein energy, dipolar distance-scaled finite-ideal gas reference, Molprobity clash, Ramachandran appearance Z-score, and rotamer Z-score. As our model builder is interfaced with CHARMM, it is advantageous to directly use other CHARMM functionality and energy functions to refine the model structures or to use the models for other computational studies using CHARMM.
Keyword
CASPCHARMMhomology modelingprotein-like scoresrestraining potential
ISSN
0192-8651
Publisher
Wiley
DOI
http://dx.doi.org/10.1002/jcc.23024
Type
Article
Appears in Collections:
Division of Biomedical Research > Disease Target Structure Research Center > 1. Journal Articles
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