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Properties of Cavities in Biological Structures—A Survey of the Protein Data Bank

2020; Frontiers Media; Volume: 7; Linguagem: Inglês

10.3389/fmolb.2020.591381

2296-889X

Mateusz Chwastyk, Ewa Panek, J. Malinowski, Mariusz Jaskólski, Marek Cieplak,

Lipid Membrane Structure and Behavior

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.