A simplified homology‐model builder toward highly protein‐like structures: An inspection of restraining potentials |
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Authors: | Tae‐Rae Kim Sangho Oh Joshua SungWoo Yang Sanghyuk Lee Seokmin Shin Jinhyuk Lee |
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Institution: | 1. Department of Chemistry, Seoul National University, Seoul 151‐747, Republic of Korea;2. Korean Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak‐ro, Yuseong‐gu, Daejeon 305‐806, Republic of Korea;3. Department of Bioinformatics, University of Science and Technology, 217 Gajung‐ro, Yuseong‐Gu, Daejeon 305‐350, Republic of Korea;4. Ewha Research Center for System Biology (ERCSB), Ewha Woman's University, 11‐1 Daehyun‐dong, Seodaemun‐gu, Seoul 120‐750, Republic of Korea;5. Department of Chemistry, Seoul National University, Seoul 151‐747, Republic of KoreaFax: (+82) 2 889 1568;6. Department of Bioinformatics, University of Science and Technology, 217 Gajung‐ro, Yuseong‐Gu, Daejeon 305‐350, Republic of KoreaFax: (+82) 42 879 8519 |
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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. |
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Keywords: | homology modeling restraining potential protein‐like scores CHARMM CASP |
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