Abstract
A smooth empirical potential is constructed for use in off-lattice protein folding studies. Our potential is a function of the ammo acid labels and of the distances between the C α atoms of a protein. The potential is a sum of smooth surface potential terms that model solvent interactions and of pair potentials that are functions of a distance, with a smooth cutoff at 12 Ångström. Techniques include the use of a fully automatic and reliable estimator for smooth densities, of cluster analysis to group together amino acid pairs with similar distance distributions, and of quadratic programming to find appropriate weights with which the various terms enter the total potential. For nine small test proteins, the new potential has local minima within 1.3-4.7Å of the PDB geometry, with one exception that has an error of 8.5Å.
The authors gratefully acknowledge support of this research by the Austrian Fond zur Förderung der wissenschaftlichen Forschung (FWF) under grant P11516-MAT.
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Neumaier, A., Dallwig, S., Huyer, W., Schichl, H. (1999). New Techniques for the Construction of Residue Potentials for Protein Folding. In: Deuflhard, P., Hermans, J., Leimkuhler, B., Mark, A.E., Reich, S., Skeel, R.D. (eds) Computational Molecular Dynamics: Challenges, Methods, Ideas. Lecture Notes in Computational Science and Engineering, vol 4. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-58360-5_12
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