Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Simultaneous identification of specifically interacting paralogs and
  inter-protein contacts by Direct-Coupling Analysis   Understanding protein-protein interactions is central to our understanding of
almost all complex biological processes. Computational tools exploiting rapidly
growing genomic databases to characterize protein-protein interactions are
urgently needed. Such methods should connect multiple scales from evolutionary
conserved interactions between families of homologous proteins, over the
identification of specifically interacting proteins in the case of multiple
paralogs inside a species, down to the prediction of residues being in physical
contact across interaction interfaces. Statistical inference methods detecting
residue-residue coevolution have recently triggered considerable progress in
using sequence data for quaternary protein structure prediction; they require,
however, large joint alignments of homologous protein pairs known to interact.
The generation of such alignments is a complex computational task on its own;
application of coevolutionary modeling has in turn been restricted to proteins
without paralogs, or to bacterial systems with the corresponding coding genes
being co-localized in operons. Here we show that the Direct-Coupling Analysis
of residue coevolution can be extended to connect the different scales, and
simultaneously to match interacting paralogs, to identify inter-protein
residue-residue contacts and to discriminate interacting from noninteracting
families in a multiprotein system. Our results extend the potential
applications of coevolutionary analysis far beyond cases treatable so far.

21
The categories of this paper are: adap-org
28
The categories of this paper are: alg-geom
27
The categories of this paper are: comp-gas
11
The categories of this paper are: hep-lat
13
The categories of this paper are: quant-ph
36
The categories of this paper are: cmp-lg
34
The categories of this paper are: chem-ph
23
The categories of this paper are: solv-int
9
The categories of this paper are: nlin
12
The categories of this paper are: nucl-th
37
The categories of this paper are: supr-con
5
The categories of this paper are: gr-qc
3
The categories of this paper are: physics
18
The categories of this paper are: econ
17
The categories of this paper are: q-fin
14
The categories of this paper are: math-ph