New tool for the interrogation of macromolecular structure

COMP 242

Francisco Torrens, Francisco.Torrens@uv.es, Institut Univesitari de Ciencia Molecular, Universitat de Valencia, Edifici d'Instituts de Paterna, P. O. Box 22085, Valencia, 46071, Spain
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 ALPHA-carbons (C^ALPHA). The coordinates obtained with BABELPDB allow characterizing the presence of hydrogen bonds (H-bond). 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 software: the calculation of the fractal dimension of lysozyme molecule with and without H atoms. The numbers compare well with reference calculations performed with our version of program GEPOL and with the results from Pfeifer et al. For proteins, C^ALPHA skeleton extracted with BABELPDB allows drawing the ribbon image, which determines the secondary structure.