Kong Lesheng, Ranganathan Shoba
Biotechnology Research Institute, Macquarie University, NSW 2109, Australia.
Brief Bioinform. 2004 Jun;5(2):179-92. doi: 10.1093/bib/5.2.179.
The delineation of domain boundaries of a given sequence in the absence of known 3D structures or detectable sequence homology to known domains benefits many areas in protein science, such as protein engineering, protein 3D structure determination and protein structure prediction. With the exponential growth of newly determined sequences, our ability to predict domain boundaries rapidly and accurately from sequence information alone is both essential and critical from the viewpoint of gene function annotation. Anyone attempting to predict domain boundaries for a single protein sequence is invariably confronted with a plethora of databases that contain boundary information available from the internet and a variety of methods for domain boundary prediction. How are these derived and how well do they work? What definition of 'domain' do they use? We will first clarify the different definitions of protein domains, and then describe the available public databases with domain boundary information. Finally, we will review existing domain boundary prediction methods and discuss their strengths and weaknesses.
在缺乏已知三维结构或与已知结构域无明显序列同源性的情况下，确定给定序列的结构域边界对蛋白质科学的许多领域都有帮助，如蛋白质工程、蛋白质三维结构测定和蛋白质结构预测。随着新测定序列呈指数增长，仅从序列信息快速准确预测结构域边界的能力，从基因功能注释的角度来看既至关重要。任何试图为单个蛋白质序列预测结构域边界的人，都必然会面临大量包含可从互联网获取的边界信息的数据库，以及各种用于结构域边界预测的方法。这些是如何推导出来的，效果如何？它们使用的“结构域”定义是什么？我们将首先阐明蛋白质结构域的不同定义，然后描述具有结构域边界信息的可用公共数据库。最后，我们将回顾现有的结构域边界预测方法，并讨论它们的优缺点。
