View : 54 Download: 0

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

Title
A simplified homology-model builder toward highly protein-like structures: An inspection of restraining potentials
Authors
Kim T.-R.Oh S.Yang J.S.Lee S.Shin S.Lee J.
Ewha Authors
이상혁
SCOPUS Author ID
이상혁scopus
Issue Date
2012
Journal Title
Journal of Computational Chemistry
ISSN
0192-8651JCR Link
Citation
vol. 33, no. 24, pp. 1927 - 1935
Indexed
SCI; SCIE; SCOPUS WOS scopus
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. © 2012 Wiley Periodicals, Inc.
DOI
10.1002/jcc.23024
Appears in Collections:
자연과학대학 > 생명과학전공 > Journal papers
Files in This Item:
There are no files associated with this item.
Export
RIS (EndNote)
XLS (Excel)
XML


qrcode

Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.

BROWSE