Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Affinity, Kinetics, and Pathways of Anisotropic Ligands Binding to
  Hydrophobic Model Pockets   Using explicit-water molecular dynamics (MD) simulations of a generic
pocket-ligand model we investigate how chemical and shape anisotropy of small
ligands influences the affinities, kinetic rates and pathways for their
association to hydrophobic binding sites. In particular, we investigate
aromatic compounds, all of similar molecular size, but distinct by various
hydrophilic or hydrophobic residues. We demonstrate that the most hydrophobic
sections are in general desolvated primarily upon binding to the cavity,
suggesting that specific hydration of the different chemical units can steer
the orientation pathways via a `hydrophobic torque'. Moreover, we find that
ligands with bimodal orientation fluctuations have significantly increased
kinetic barriers for binding compared to the kinetic barriers previously
observed for spherical ligands due to translational fluctuations. We exemplify
that these kinetic barriers, which are ligand specific, impact both binding and
unbinding times for which we observe considerable differences between our
studied ligands.

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The categories of this paper are: bayes-an
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The categories of this paper are: chem-ph
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The categories of this paper are: q-alg
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The categories of this paper are: dg-ga
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The categories of this paper are: comp-gas
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The categories of this paper are: math-ph
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The categories of this paper are: gr-qc
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The categories of this paper are: alg-geom
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The categories of this paper are: chao-dyn
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The categories of this paper are: mtrl-th
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The categories of this paper are: math
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The categories of this paper are: adap-org
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The categories of this paper are: cmp-lg
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The categories of this paper are: q-fin
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The categories of this paper are: hep-lat
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The categories of this paper are: solv-int