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A new Tool for the Interrogation of Macromolecular Structure
* 1 , 2
1  Institut Universitari de Ciencia Molecular, Universitat de Valencia
2  Departamento de Ciencias Experimentales y Matemáticas, Facultad de Veterinaria y Ciencias Experimentales, Universidad Católica de Valencia "San Vicente Mártir"

Abstract: Our program BABELPDB allows browsing and interrogating the native and derived structural features of biological macromolecules using data obtained from the Protein Data Bank (PDB). Major features of BABELPDB are: (1) convert from PDB to other formats, (2) add or remove H atoms, (3) strip the crystallization water molecules and (4) separate the a‑carbons (Ca). The coordinates obtained with BABELPDB permit characterizing the presence of hydrogen bonds (H‑bonds). The algorithm for detecting H‑bonds is implemented in our program TOPO for the theoretical simulation of the molecular shape. An example is given to illustrate the capabilities of the software: the calculation of the fractal dimension of the lysozyme molecule with (1.908) and without (1.920) H atoms. The numbers compare well with reference calculations performed with our version of the GEPOL program and with the results from Pfeifer et al. For proteins, the Ca skeleton extracted with BABELPDB allows drawing the ribbon image, which determines the secondary structure of proteins.
Keywords: Information retrieval, Chemical structure, Secondary structure, Solvation water,  Carbon skeleton, Hydrogen bond, Molecular shape, Fractal dimension, Protein database, Protein Data Bank, Property visualization