A simplified homology-model builder toward highly protein-like structures: An inspection of restraining potentials
| Autor: | Sangho Oh, Jinhyuk Lee, Sanghyuk Lee, Seokmin Shin, Joshua SungWoo Yang, Tae Rae Kim |
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| Rok vydání: | 2012 |
| Předmět: |
Models
Molecular Proteomics Computer science Molecular Sequence Data Stability (learning theory) Computational science Humans Amino Acid Sequence Homology modeling Databases Protein CASP Simulation Caspase 7 Quantitative Biology::Biomolecules Sequence Homology Amino Acid MODELLER General Chemistry Quadratic function Caspase 9 Computational Mathematics Discrete optimized protein energy Benchmark (computing) Thermodynamics Algorithms Software Ramachandran plot |
| Zdroj: | Journal of Computational Chemistry. 33:1927-1935 |
| ISSN: | 0192-8651 |
| DOI: | 10.1002/jcc.23024 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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