A NEW APPROACH TO HOMOLOGY MODELING

Abstract

The need to interpret experimental results led to, first, an all-atom force field, followed by a coarse-grained one. As an aid to these force fields, a new approach is introduced here to predict protein structure based on the physical properties of the amino acids. This approach includes three key components: Kidera factors describing the physical properties, Fourier transformation and UNRES coarse grained force field simulations. Different from traditional homology modeling methods which are based on evolution, this approach is physics-based, and does not have the same weaknesses as the traditional homology modeling methods. Our results show that this approach can produce above average prediction results, and can be used as a useful tool for protein structure prediction.

Keywords

• protein structure prediction
• physical properties
• Kidera factors
• Fourier transformation
• coarse-grained force field