Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: An Exact Algorithm for Side-Chain Placement in Protein Design   Computational protein design aims at constructing novel or improved functions
on the structure of a given protein backbone and has important applications in
the pharmaceutical and biotechnical industry. The underlying combinatorial
side-chain placement problem consists of choosing a side-chain placement for
each residue position such that the resulting overall energy is minimum. The
choice of the side-chain then also determines the amino acid for this position.
Many algorithms for this NP-hard problem have been proposed in the context of
homology modeling, which, however, reach their limits when faced with large
protein design instances.
  In this paper, we propose a new exact method for the side-chain placement
problem that works well even for large instance sizes as they appear in protein
design. Our main contribution is a dedicated branch-and-bound algorithm that
combines tight upper and lower bounds resulting from a novel Lagrangian
relaxation approach for side-chain placement. Our experimental results show
that our method outperforms alternative state-of-the art exact approaches and
makes it possible to optimally solve large protein design instances routinely.

6
The categories of this paper are: astro-ph
27
The categories of this paper are: comp-gas
13
The categories of this paper are: quant-ph
0
The categories of this paper are: hep-ph
3
The categories of this paper are: physics
33
The categories of this paper are: plasm-ph
31
The categories of this paper are: ao-sci
14
The categories of this paper are: math-ph
32
The categories of this paper are: atom-ph
26
The categories of this paper are: bayes-an
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The categories of this paper are: gr-qc
25
The categories of this paper are: patt-sol
8
The categories of this paper are: hep-ex
10
The categories of this paper are: q-bio
17
The categories of this paper are: q-fin
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The categories of this paper are: stat