生物结构中腔的特性——蛋白质数据库综述

Chwastyk Mateusz, Panek Ewa A, Malinowski Jan, Jaskólski Mariusz, Cieplak Marek

Institute of Physics, Polish Academy of Sciences, Warsaw, Poland.

Department of Biometry, Warsaw University of Life Sciences, Warsaw, Poland.

Front Mol Biosci. 2020 Nov 6;7:591381. doi: 10.3389/fmolb.2020.591381. eCollection 2020.

We performed a PDB-wide survey of proteins to assess their cavity content, using the SPACEBALL algorithm to calculate the cavity volumes. In addition, we determined the hydropathy character of the cavities. We demonstrate that the cavities of most proteins are hydrophilic, but smaller proteins tend to have cavities with hydrophobic walls. We propose criteria for distinguishing between cavities and pockets, and single out proteins with the largest cavities.

我们对蛋白质数据库（PDB）中的所有蛋白质进行了一项调查，以评估其空腔含量，使用SPACEBALL算法计算空腔体积。此外，我们还确定了这些空腔的亲水性特征。我们证明，大多数蛋白质的空腔是亲水的，但较小的蛋白质往往具有带有疏水壁的空腔。我们提出了区分空腔和口袋的标准，并挑选出具有最大空腔的蛋白质。