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1 TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

1 2014

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A new approach to homology modeling

He Y., Scheraga H. A., Rackovsky S.

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

2014

Vol. 18, No 3

211--128

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