Residue-residue mean-force potentials for protein structure recognition |
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Authors: | Reva BA; Finkelstein AV; Sanner MF; Olson AJ |
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Affiliation: | Department of Molecular Biology, Scripps Research Institute, CA 92037, USA. |
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Abstract: | We present two new sets of energy functions for protein structure
recognition, given the primary sequence of amino acids along the
polypeptide chain. The first set of potentials is based on the positions of
alpha- and the second on positions of beta- and alpha- carbon atoms of
amino acid residues. The potentials are derived using a theory of
Boltzmann-like statistics of protein structure. The energy terms
incorporate both long-range interactions between residues remote along a
chain and short-range interactions between near neighbors. Distance
dependence is approximated by a piecewise constant function defined on
intervals of equal size. The size of the interval is optimized to preserve
as much detail as possible without introducing excessive error due to
limited statistics. A database of 214 non- homologous proteins was used
both for the derivation of the potentials, and for the 'threading' test
originally suggested by Hendlich et al. (1990) J. Mol. Biol., 216, 167-180.
Special care is taken to avoid systematic error in this test. For
threading, we used 100 non- homologous protein chains of 60-205 residues.
The energy of each of the native structures was compared with the energy of
43,000 to 19,000 alternative structures generated by threading. Of these
100 native structures, 92 have the lowest energy with alpha-carbon-based
potentials and, even more, 98 of these 100 structures, have the lowest
energy with the beta- and alpha-carbon based potentials.
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