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This Protein Nano-Object Integrator (ProNOI) software allows for researchers to generate atomic-style geometrical objects in the desired shape and dimensions either from cry-electron photography or user-specified shape. Biomolecular modeling is important to address biological problems at the molecular level and to understand the interactions between molecules to predict behavior. This is especially useful for pharmaceutical development and within the general research community. Biological macromolecules must frequently be modeled in conjunction with nano-objects in order to understand their interactions. However, nano-objects are typically unavailable in commonly used modeling systems and the customization of these objects can be limited. Clemson University researchers have developed the versatile Protein Nano-Object Integrator (ProNOI) software which allows for modeling of nano-objects with biological macromolecules. An unlimited number of customizable objects can be created and combined with biological macromolecules. The objects can be tailored in regards to their position, size, shape, distributed charge, and surface or volumetric parameters depending on the user’s needs.
Pharmaceutical development; institutional research
The ProNOI software provides a convenient and user-friendly method for simulating surfaces and regular objects. An unlimited number of objects can be created and combined with biological macromolecules in the Protein Data Bank (PDB) format file. Once the objects are generated, the user can use sliders to manipulate their shape, dimension and absolute position. In addition, the software offers the option to charge the objects with either specified surface or volumetric charge density and to model them with user-desired dielectric constants. According to the user’s preference, the biological macromolecule atoms can be assigned charges and radii with four force fields, including Amber, Charmm, OPLS and PARSE. Furthermore, the output file is compatible with most biophysical software.
Nicholas Smith, Emil Alexov
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