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A simplified homology-model builder toward highly protein-like structures: an inspection of restraining potentials.
Kim, Tae-Rae; Oh, Sangho; Yang, Joshua SungWoo; Lee, Sanghyuk; Shin, Seokmin; Lee, Jinhyuk.
Afiliação
  • Kim TR; Department of Chemistry, Seoul National University, Seoul 151-747, Republic of Korea.
J Comput Chem ; 33(24): 1927-35, 2012 Sep 15.
Article em En | MEDLINE | ID: mdl-22648914
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.
Assuntos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Software / Homologia de Sequência de Aminoácidos / Proteômica / Caspase 7 / Caspase 9 Tipo de estudo: Prognostic_studies Limite: Humans Idioma: En Ano de publicação: 2012 Tipo de documento: Article

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Software / Homologia de Sequência de Aminoácidos / Proteômica / Caspase 7 / Caspase 9 Tipo de estudo: Prognostic_studies Limite: Humans Idioma: En Ano de publicação: 2012 Tipo de documento: Article