A New Tool for the Interrogation of Macromolecular Structure in Chemical Education

Program BABELPDB allows browsing–interrogating native–derived structural features of biological macromolecules using data obtained from the Protein Data Bank (PDB). Major features are: (1) convert from PDB to other formats, (2) add H atoms, (3) strip water molecules and (4) separate a-carbons (Ca). The coordinates obtained with BABELPDB allow characterizing the presence of Hbonds. The algorithm for detecting H-bonds is implemented in program TOPO for the theoretical simulation of the molecular shape. An example illustrates the capabilities, i.e., calculation of the fractal dimension of lysozyme (1.908) with and without (1.920) H atoms. The numbers compare with reference calculations performed with program GEPOL and results from Pfeifer et al. For proteins, Ca skeleton allows drawing the ribbons image, which determines the secondary structure.