Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Interactive molecular dynamics in virtual reality for accurate flexible
  protein-ligand docking   Simulating drug binding and unbinding is a challenge, as the rugged energy
landscapes that separate bound and unbound states require extensive sampling
that consumes significant computational resources. Here, we describe the use of
interactive molecular dynamics in virtual reality (iMD-VR) as an accurate
low-cost strategy for flexible protein-ligand docking. We outline an
experimental protocol which enables expert iMD-VR users to guide ligands into
and out of the binding pockets of trypsin, neuraminidase, and HIV-1 protease,
and recreate their respective crystallographic protein-ligand binding poses
within 5 - 10 minutes. Following a brief training phase, our studies shown that
iMD-VR novices were able to generate unbinding and rebinding pathways on
similar timescales as iMD-VR experts, with the majority able to recover binding
poses within 2.15 Angstrom RMSD of the crystallographic binding pose. These
results indicate that iMD-VR affords sufficient control for users to carry out
the detailed atomic manipulations required to dock flexible ligands into
dynamic enzyme active sites and recover crystallographic poses, offering an
interesting new approach for simulating drug docking and generating binding
hypotheses.

12
The categories of this paper are: nucl-th
32
The categories of this paper are: atom-ph
24
The categories of this paper are: dg-ga
35
The categories of this paper are: mtrl-th
28
The categories of this paper are: alg-geom
33
The categories of this paper are: plasm-ph
30
The categories of this paper are: q-alg
13
The categories of this paper are: quant-ph
1
The categories of this paper are: cs
22
The categories of this paper are: chao-dyn
34
The categories of this paper are: chem-ph
15
The categories of this paper are: nucl-ex
4
The categories of this paper are: cond-mat
0
The categories of this paper are: hep-ph
26
The categories of this paper are: bayes-an
20
The categories of this paper are: acc-phys