Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Modeling of protein-peptide interactions using the CABS-dock web server
  for binding site search and flexible docking   Protein-peptide interactions play essential functional roles in living
organisms and their structural characterization is a hot subject of current
experimental and theoretical research. Computational modeling of the structure
of protein-peptide interactions is usually divided into two stages: prediction
of the binding site at a protein receptor surface, and then docking (and
modeling) the peptide structure into the known binding site. This paper
presents a comprehensive CABS-dock method for the simultaneous search of
binding sites and flexible protein-peptide docking, available as a users
friendly web server. We present example CABS-dock results obtained in the
default CABS-dock mode and using its advanced options that enable the user to
increase the range of flexibility for chosen receptor fragments or to exclude
user-selected binding modes from docking search. Furthermore, we demonstrate a
strategy to improve CABS-dock performance by assessing the quality of models
with classical molecular dynamics. Finally, we discuss the promising extensions
and applications of the CABS-dock method and provide a tutorial appendix for
the convenient analysis and visualization of CABS-dock results. The CABS-dock
web server is freely available at http://biocomp.chem.uw.edu.pl/CABSdock/

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The categories of this paper are: patt-sol
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The categories of this paper are: adap-org
34
The categories of this paper are: chem-ph
27
The categories of this paper are: comp-gas
9
The categories of this paper are: nlin
37
The categories of this paper are: supr-con
36
The categories of this paper are: cmp-lg
0
The categories of this paper are: hep-ph
2
The categories of this paper are: math
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The categories of this paper are: eess
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The categories of this paper are: q-fin
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The categories of this paper are: acc-phys
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The categories of this paper are: alg-geom
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The categories of this paper are: atom-ph
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The categories of this paper are: physics
11
The categories of this paper are: hep-lat