Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA.
Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA.
J Struct Biol. 2018 Nov;204(2):313-318. doi: 10.1016/j.jsb.2018.08.004. Epub 2018 Aug 13.
The EMDataBank Validation Challenge was a challenging task for students newly introduced to the cryoEM and molecular modeling fields. However, the competition provided an effective space for student modelers to discover and explore the potentials of atomic modeling and refinement by practicing on published atomic structures. Here, by employing manual molecular modeling programs such as Coot, Phenix, and Chimera, we have regularized and improved three targets. The T20S proteasome and TRPV1 ion channel allowed us to broaden our understanding of these modeling techniques while the 70S ribosome served as a challenge to test the limits of our abilities. We were successful in our efforts to improve each of the models and provide here our cohesive methodology for de novo modeling with and without homology models, which may serve as a starting point for other undergraduates and researchers just entering the realm of cryoEM. Additionally, we provide some constructive criticism to facilitate the introduction of said undergraduates and researchers into cryoEM in the future.
EMDataBank 验证挑战赛对于刚接触冷冻电镜和分子建模领域的学生来说是一项具有挑战性的任务。然而，该竞赛为学生建模者提供了一个有效的空间，让他们通过对已发表的原子结构进行实践，发现和探索原子建模和精修的潜力。在这里，我们使用了 Coot、Phenix 和 Chimera 等手动分子建模程序，对三个目标进行了正则化和改进。T20S 蛋白酶体和 TRPV1 离子通道使我们能够拓宽对这些建模技术的理解，而 70S 核糖体则作为一个挑战，以测试我们能力的极限。我们成功地改进了每个模型，并在此提供了从头建模的综合方法，包括有无同源模型，这可能为其他刚进入冷冻电镜领域的本科生和研究人员提供一个起点。此外，我们提供了一些建设性的批评意见，以促进未来有本科生和研究人员进入冷冻电镜领域。
