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Title 

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

Authors 

T R KimSangho OhJoshua Sungwoo YangSanghyuk LeeS ShinJinhyuk Lee

Publisher 

Wiley-Blackwell

Issue Date 

2012

Citation 

Journal of Computational Chemistry, vol. 33, no. 24, pp. 1927-1935

Keywords 

CASPCHARMMhomology modelingprotein-like scoresrestraining potential

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.

ISSN 

0192-8651

Link 

http://dx.doi.org/10.1002/jcc.23024

Appears in Collections

1. Journal Articles > Journal Articles

Registered Date

2017-04-19


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