Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Amino-acid-dependent main-chain torsion-energy terms for protein systems   Many commonly used force fields for protein systems such as AMBER, CHARMM,
GROMACS, OPLS, and ECEPP have amino-acid-independent force-field parameters of
main-chain torsion-energy terms. Here, we propose a new type of
amino-acid-dependent torsion-energy terms in the force fields. As an example,
we applied this approach to AMBER ff03 force field and determined new
amino-acid-dependent parameters for $\psi$ and $\psi'$ angles for each amino
acid by using our optimization method, which is one of the knowledge-based
approach. In order to test the validity of the new force-field parameters, we
then performed folding simulations of $\alpha$-helical and $\beta$-hairpin
peptides, using the optimized force field. The results showed that the new
force-field parameters gave structures more consistent with the experimental
implications than the original AMBER ff03 force field.

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The categories of this paper are: comp-gas
36
The categories of this paper are: cmp-lg
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The categories of this paper are: math-ph
17
The categories of this paper are: q-fin
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The categories of this paper are: chao-dyn
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The categories of this paper are: alg-geom
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The categories of this paper are: nucl-th
31
The categories of this paper are: ao-sci
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The categories of this paper are: nlin
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The categories of this paper are: patt-sol
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The categories of this paper are: hep-th
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The categories of this paper are: atom-ph
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The categories of this paper are: eess
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The categories of this paper are: dg-ga
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The categories of this paper are: plasm-ph
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The categories of this paper are: q-alg