A. Pedretti,  L. Villa,  G. Vistoli

UniversitÓ degli Studi di Milano Istituto di Chimica Farmaceutica e Tossicologica - Milan University
Viale Abruzzi, 42 - I-20131 Milano (Italy)


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1. Introduction
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One of the fundamental quest in computational chemistry is to constantly ease the interchange of the data. This requirement becomes more and more strong with the increasing of the number of file formats, that invaded the world of molecular modelling. Currently every software has its specific file format and  often the molecular modelling packages cannot directly exchange information, because their molecular files are incompatible each other.

Moreover, due to the diffusion of the force fields, one could want to maintain the same format, but to change the force field by reassigning the atom types with a new atom classification. Several classifications (force fields) have been proposed to classify the atoms into atom types based on atomic number, hybridization, bond order and bonded partners and every classification uses specific symbolic codes to represent its atom types (1) (2).

The PDB file format (3) is become the leading format for the storage of biomacromolecules due to the explosion of experimental resolved structures deposited in Brookhaven Data Bank. Therefore the PDB format is maybe the only type recognized by almost all molecular modelling packages. Unfortunately PDB files don’t include any information about atom types or atomic charges and it is a limiting step for structure modelling and for analysis of receptor-ligand interactions.

Indeed VEGA is born to handle PDB files with BioDock (4), our stochastic docking program, without using other softwares to assign atom parameters. With time the goals of VEGA raise and now it’s become a versatile tool able to convert numerous file formats, to assign the atom types and atomic charges using several force field templates, to calculate molecular surfaces and to determine several molecular properties.


VEGA schematics

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2. Visualization   Next page