Journal ID (nlm-ta): PLoS One
Journal ID (iso-abbrev): PLoS ONE
Journal ID (publisher-id): plos
Journal ID (pmc): plosone
Title:
PLoS ONE
Publisher:
Public Library of Science
(San Francisco, CA USA
)
ISSN
(Electronic):
1932-6203
Publication date
(Electronic):
11
March
2020
Publication date Collection: 2020
Volume: 15
Issue: 3
Electronic Location Identifier: e0228461
Affiliations
[1
]
Intangible Realities Laboratory, School of Chemistry, University of Bristol, Bristol,
England, United Kingdom
[2
]
Department of Computer Science, University of Bristol, Bristol, England, United Kingdom
[3
]
Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol,
England, United Kingdom
University of Leeds, UNITED KINGDOM
Author notes
Competing Interests: DRG acknowledges cloud computing resources were provided from Oracle Corporation via
a Bristol University Partnership Cloud award. This does not alter our adherence to
PLOS ONE policies on sharing data and materials. There are no patents, products in
development or marketed products to declare.
Author information
Article
Publisher ID:
PONE-D-19-26973
DOI: 10.1371/journal.pone.0228461
PMC ID: 7065745
PubMed ID: 32160194
SO-VID: 9548a765-de8f-4f65-af81-8ccb140fbd0e
Copyright © © 2020 Deeks et al
License:
This is an open access article distributed under the terms of the
Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided
the original author and source are credited.
Funded by: funder-id http://dx.doi.org/10.13039/501100000266, Engineering and Physical Sciences Research Council;
Award ID: DTA
Award Recipient
:
Helen M. Deeks
Funded by: funder-id http://dx.doi.org/10.13039/501100000266, Engineering and Physical Sciences Research Council;
Award ID: DTA-2
Award Recipient
:
Rebecca K. Walters
Funded by: royal society
Award ID: RGF\EA\181075
Award Recipient
:
Michael B. O’Connor
Funded by: funder-id http://dx.doi.org/10.13039/501100000268, Biotechnology and Biological Sciences Research Council;
Award ID: BB/R00661X/1
Award Recipient
:
Michael B. O’Connor
Funded by: funder-id http://dx.doi.org/10.13039/501100000266, Engineering and Physical Sciences Research Council;
Award ID: EP/P021123/1
Award Recipient
:
ORCID: http://orcid.org/0000-0003-3153-143X
Stephanie R. Hare
Funded by: funder-id http://dx.doi.org/10.13039/501100000266, Engineering and Physical Sciences Research Council;
Award ID: EPSRC
Award Recipient
:
Adrian J. Mulholland
Funded by: funder-id http://dx.doi.org/10.13039/501100000266, Engineering and Physical Sciences Research Council;
Award ID: CCP-BioSim
Award Recipient
:
Adrian J. Mulholland
Funded by: royal society
Award ID: URF\R\180033
Award Recipient
:
ORCID: http://orcid.org/0000-0002-9608-3845
David R. Glowacki
Funded by: funder-id http://dx.doi.org/10.13039/501100000266, Engineering and Physical Sciences Research Council;
Award ID: EP/P021123/1
Award Recipient
:
ORCID: http://orcid.org/0000-0002-9608-3845
David R. Glowacki
Funded by: funder-id http://dx.doi.org/10.13039/501100000275, Leverhulme Trust;
Award ID: philip Leverhulme award
Award Recipient
:
ORCID: http://orcid.org/0000-0002-9608-3845
David R. Glowacki
HMD and RKW are funded by PhD studentships from Engineering and Physical Sciences
Research Council (EPSRC). MOC is supported through the Royal Society (RGF\EA\181075)
and BBSRC (BB/R00661X/1). SRH is funded by EPSRC programme grant EP/P021123/1. AJM
thanks EPSRC for funding (EP/M022609/1) and also the Collaborative Computational Project
for Biomolecular Simulation (CCP-BioSim,
www.ccpbiosim.ac.uk), supported by EPSRC. DRG acknowledges funding from: Oracle Corporation (University
Partnership Cloud award); the Royal Society (URF\R\180033); EPSRC (impact acceleration
award, institutional sponsorship award, and EP/P021123/1), and the Leverhulme Trust
(Philip Leverhulme Prize). Cloud computing resources, enabling us to run some of the
simulations described herein, were provided from Oracle Corporation via a Bristol
University Partnership Cloud award. None of the authors received any form of support
from Oracle in the form of salary. The funders had no role in study design, data collection
and analysis, decision to publish, or preparation of the manuscript.
Subject:
Research Article
Subject:
Biology and Life Sciences
Subject:
Biochemistry
Subject:
Enzymology
Subject:
Enzymes
Subject:
Proteases
Subject:
Biology and Life Sciences
Subject:
Biochemistry
Subject:
Proteins
Subject:
Enzymes
Subject:
Proteases
Subject:
Biology and Life Sciences
Subject:
Microbiology
Subject:
Medical Microbiology
Subject:
Microbial Pathogens
Subject:
Viral Pathogens
Subject:
Immunodeficiency Viruses
Subject:
HIV
Subject:
HIV-1
Subject:
Medicine and Health Sciences
Subject:
Pathology and Laboratory Medicine
Subject:
Pathogens
Subject:
Microbial Pathogens
Subject:
Viral Pathogens
Subject:
Immunodeficiency Viruses
Subject:
HIV
Subject:
HIV-1
Subject:
Biology and Life Sciences
Subject:
Organisms
Subject:
Viruses
Subject:
Viral Pathogens
Subject:
Immunodeficiency Viruses
Subject:
HIV
Subject:
HIV-1
Subject:
Biology and Life Sciences
Subject:
Organisms
Subject:
Viruses
Subject:
Immunodeficiency Viruses
Subject:
HIV
Subject:
HIV-1
Subject:
Biology and life sciences
Subject:
Organisms
Subject:
Viruses
Subject:
RNA viruses
Subject:
Retroviruses
Subject:
Lentivirus
Subject:
HIV
Subject:
HIV-1
Subject:
Biology and Life Sciences
Subject:
Microbiology
Subject:
Medical Microbiology
Subject:
Microbial Pathogens
Subject:
Viral Pathogens
Subject:
Retroviruses
Subject:
Lentivirus
Subject:
HIV
Subject:
HIV-1
Subject:
Medicine and Health Sciences
Subject:
Pathology and Laboratory Medicine
Subject:
Pathogens
Subject:
Microbial Pathogens
Subject:
Viral Pathogens
Subject:
Retroviruses
Subject:
Lentivirus
Subject:
HIV
Subject:
HIV-1
Subject:
Biology and Life Sciences
Subject:
Organisms
Subject:
Viruses
Subject:
Viral Pathogens
Subject:
Retroviruses
Subject:
Lentivirus
Subject:
HIV
Subject:
HIV-1
Subject:
Biology and Life Sciences
Subject:
Biochemistry
Subject:
Enzymology
Subject:
Enzymes
Subject:
Proteases
Subject:
Serine Proteases
Subject:
Biology and Life Sciences
Subject:
Biochemistry
Subject:
Proteins
Subject:
Enzymes
Subject:
Proteases
Subject:
Serine Proteases
Subject:
Biology and Life Sciences
Subject:
Biochemistry
Subject:
Biochemical Simulations
Subject:
Biology and Life Sciences
Subject:
Computational Biology
Subject:
Biochemical Simulations
Subject:
Physical Sciences
Subject:
Chemistry
Subject:
Computational Chemistry
Subject:
Molecular Dynamics
Subject:
Physical Sciences
Subject:
Chemistry
Subject:
Physical Chemistry
Subject:
Chemical Bonding
Subject:
Hydrogen Bonding
Subject:
Physical Sciences
Subject:
Chemistry
Subject:
Chemical Compounds
Subject:
Organic Compounds
Subject:
Amino Acids
Subject:
Acidic Amino Acids
Subject:
Aspartic Acid
Subject:
Physical Sciences
Subject:
Chemistry
Subject:
Organic Chemistry
Subject:
Organic Compounds
Subject:
Amino Acids
Subject:
Acidic Amino Acids
Subject:
Aspartic Acid
Subject:
Biology and Life Sciences
Subject:
Biochemistry
Subject:
Proteins
Subject:
Amino Acids
Subject:
Acidic Amino Acids
Subject:
Aspartic Acid
Subject:
Biology and Life Sciences
Subject:
Psychology
Subject:
Addiction
Subject:
Addicts
Subject:
Drug Users
Subject:
Social Sciences
Subject:
Psychology
Subject:
Addiction
Subject:
Addicts
Subject:
Drug Users