Background: With the progress of nanotechnology, one frequently has to model biological macromolecules\r\nsimultaneously with nano-objects. However, the atomic structures of the nano objects are typically not available or\r\nthey are solid state entities. Because of that, the researchers have to investigate such nano systems by generating\r\nmodels of the nano objects in a manner that the existing software be able to carry the simulations. In addition, it\r\nshould allow generating composite objects with complex shape by combining basic geometrical figures and\r\nembedding biological macromolecules within the system.\r\nResults: Here we report the Protein Nano-Object Integrator (ProNOI) which allows for generating atomic-style\r\ngeometrical objects with user desired shape and dimensions. Unlimited number of objects can be created and\r\ncombined with biological macromolecules in Protein Data Bank (PDB) format file. Once the objects are generated,\r\nthe users can use sliders to manipulate their shape, dimension and absolute position. In addition, the software\r\noffers the option to charge the objects with either specified surface or volumetric charge density and to model\r\nthem with user-desired dielectric constants. According to the user preference, the biological macromolecule atoms\r\ncan be assigned charges and radii according to four different force fields: Amber, Charmm, OPLS and PARSE. The\r\nbiological macromolecules and the atomic-style objects are exported as a position, charge and radius (PQR) file, or\r\nif a default dielectric constant distribution is not selected, it is exported as a position, charge, radius and epsilon\r\n(PQRE) file. As illustration of the capabilities of the ProNOI, we created a composite object in a shape of a robot,\r\naptly named the Clemson Robot, whose parts are charged with various volumetric charge densities and holds the\r\nbarnase-barstar protein complex in its hand.\r\nConclusions: The Protein Nano-Object Integrator (ProNOI) is a convenient tool for generating atomic-style nano\r\nshapes in conjunction with biological macromolecule(s). Charges and radii on the macromolecule atoms and the\r\natoms in the shapes are assigned according to the user�s preferences allowing various scenarios of modeling. The\r\ndefault output file is in PQR (PQRE) format which is readable by almost any software available in biophysical field. It\r\ncan be downloaded from: http://compbio.clemson.edu/downloadDir/ProNO_integrator.tar.gz
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