Sterpone Fabio, Melchionna Simone, Tuffery Pierre, Pasquali Samuela, Mousseau Normand, Cragnolini Tristan, Chebaro Yassmine, St-Pierre Jean-Francois, Kalimeri Maria, Barducci Alessandro, Laurin Yoann, Tek Alex, Baaden Marc, Nguyen Phuong Hoang, Derreumaux Philippe
Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005, Paris, France.
Chem Soc Rev. 2014 Jul 7;43(13):4871-93. doi: 10.1039/c4cs00048j. Epub 2014 Apr 23.
The OPEP coarse-grained protein model has been applied to a wide range of applications since its first release 15 years ago. The model, which combines energetic and structural accuracy and chemical specificity, allows the study of single protein properties, DNA-RNA complexes, amyloid fibril formation and protein suspensions in a crowded environment. Here we first review the current state of the model and the most exciting applications using advanced conformational sampling methods. We then present the current limitations and a perspective on the ongoing developments.
自15年前首次发布以来,OPEP粗粒度蛋白质模型已被广泛应用于各种领域。该模型结合了能量和结构准确性以及化学特异性,能够研究单个蛋白质特性、DNA-RNA复合物、淀粉样纤维形成以及拥挤环境中的蛋白质悬浮液。在这里,我们首先回顾该模型的当前状态以及使用先进构象采样方法的最令人兴奋的应用。然后,我们介绍当前的局限性以及对正在进行的发展的展望。