Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Coupling enhanced sampling of the apo-receptor with template-based
  ligand conformers selection: Performance in pose prediction in the D3R-GC4   We report the performance of our newly introduced Ensemble Docking with
Enhanced sampling of pocket Shape (EDES) protocol coupled to a template-based
algorithm to generate near-native ligand conformations in the 2019 iteration of
the Grand Challenge organized by the D3R consortium. Using either AutoDock4.2
or HADDOCK2.2 docking programs (each software in two variants of the protocol)
our method generated native-like poses among the top 5 submitted for evaluation
for most of the 20 targets with similar performances. The protein selected for
GC4 was the human beta-site amyloid precursor protein cleaving enzyme 1
(BACE-1), a transmembrane aspartic-acid protease. We identified at least one
pose whose heavy-atoms RMSD was less than 2.5 {\AA} from the native
conformation for 16 (80%) and 17 (85%) of the twenty targets using AutoDock and
HADDOCK, respectively. Dissecting the possible sources of errors revealed that:
i) our EDES protocol (with minor modifications) was able to sample
sub-{\aa}ngstrom conformations for all 20 protein targets, reproducing the
correct conformation of the binding site within ~1 {\AA} RMSD; ii) as already
shown by some of us in GC3, even in the presence of near-native protein
structures, a proper selection of ligand conformers is crucial for the success
of ensemble-docking calculations. Importantly, our approach performed best
among the protocols exploiting only structural information of the apo protein
to generate conformations of the receptor for ensemble-docking calculations.

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The categories of this paper are: funct-an
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The categories of this paper are: chem-ph
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The categories of this paper are: q-fin
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The categories of this paper are: quant-ph
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The categories of this paper are: solv-int
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The categories of this paper are: nucl-th
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The categories of this paper are: physics
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The categories of this paper are: stat
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The categories of this paper are: ao-sci
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The categories of this paper are: mtrl-th
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The categories of this paper are: dg-ga
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The categories of this paper are: supr-con
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The categories of this paper are: adap-org
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The categories of this paper are: econ
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The categories of this paper are: chao-dyn
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The categories of this paper are: hep-ex