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{{Short description|Software for computational chemistry}}
{{multiple issues|
{{multiple issues|
{{COI|date=October 2013}}
{{COI|date=October 2013}}
{{news release|date=October 2013}}
{{news release|date=October 2013}}
{{Primary sources|date=November 2019}}
}}
}}

{{Infobox software
{{Infobox software
|name = Desmond
|name = Desmond
|developer = [[D. E. Shaw Research]]
|developer = [[D. E. Shaw Research]]
|operating system = [[Linux]]
|operating system = [[Linux]]
|platform = [[x86]], [[x86-64]], [[computer cluster]]s
|platform = [[x86]], [[x86-64]], [[computer cluster]]s
|size =
|size =
|language = English
|language = English
|genre = [[Computational chemistry]]
|genre = [[Computational chemistry]]
|license = [[Proprietary software|Proprietary]] [[freeware]], [[commercial software]]
|license = [[Proprietary software|Proprietary]] [[freeware]], [[commercial software]]
|website = {{URL|www.deshawresearch.com/resources_desmond.html}}, {{URL|www.schrodinger.com/products/14/3}}
|website = {{URL|www.deshawresearch.com/resources_desmond.html}}, {{URL|schrodinger.com/desmond}}
}}
}}
'''Desmond''' is a software package developed at [[D. E. Shaw Research]] to perform high-speed [[molecular dynamics]] simulations of biological systems on conventional [[computer cluster]]s.<ref>{{cite journal|
'''Desmond''' is a software package developed at [[D. E. Shaw Research]] to perform high-speed [[molecular dynamics]] simulations of biological systems on conventional [[computer cluster]]s.<ref>{{cite book
|chapter-url=http://sc06.supercomputing.org/schedule/pdf/pap259.pdf
publisher=[[Association for Computing Machinery|ACM]]|author1=Kevin J. Bowers |author2=Edmond Chow |author3=Huafeng Xu |author4=Ron O. Dror |author5=Michael P. Eastwood |author6=Brent A. Gregersen |author7=John L. Klepeis |author8=István Kolossváry |author9=Mark A. Moraes |author10=Federico D. Sacerdoti |author11=John K. Salmon |author12=Yibing Shan |author13=David E. Shaw |
|doi=10.1109/SC.2006.54
title=Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters|
|isbn=978-0-7695-2700-0
url=http://sc06.supercomputing.org/schedule/pdf/pap259.pdf|
|chapter=Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters
isbn=0-7695-2700-0|
|title=ACM/IEEE SC 2006 Conference (SC'06)
journal=Proceedings of the ACM/IEEE Conference on Supercomputing (SC06), Tampa, Florida, November 11–17, 2006.|
|pages=43
year=2006
|year=2006
}}</ref><ref>{{cite journal|
|last1=Bowers
publisher=[[PNAS]]|author1=Morten Ø. Jensen |author2=David W. Borhani |author3=Kresten Lindorff-Larsen |author4=Paul Maragakis |author5=Vishwanath Jogini |author6=Michael P. Eastwood |author7=Ron O. Dror |author8=David E. Shaw |
|first1=Kevin J.
title=Principles of Conduction and Hydrophobic Gating in K+ Channels|
|last2=Chow
url=http://www.pnas.org/content/107/13/5833.full|
|first2=Edmond
journal=Proceedings of the National Academy of Sciences of the United States of America|
|last3=Xu
volume= 107|
|first3=Huafeng
pages= 5833–5838|
|last4=Dror
doi=10.1073/pnas.0911691107|
|first4=Ron O.
year=2010|
|last5=Eastwood
pmid=20231479|
|first5=Michael P.
issue=13|
|last6=Gregersen
pmc=2851896
|first6=Brent A.
}}</ref><ref>{{cite journal|
|last7=Klepeis
publisher=[[PNAS]]|author1=Ron O. Dror |author2=Daniel H. Arlow |author3=David W. Borhani |author4=Morten Ø. Jensen |author5=Stefano Piana |author6=David E. Shaw |
|first7=John L.
title=Identification of Two Distinct Inactive Conformations of the ß2-Adrenergic Receptor Reconciles Structural and Biochemical Observations|
|last8=Kolossvary
url=http://www.pnas.org/content/106/12/4689.full|
|first8=Istvan
doi=10.1073/pnas.0811065106|
|last9=Moraes
journal=Proceedings of the National Academy of Sciences of the United States of America|
|first9=Mark A.
volume= 106|
|last10=Sacerdoti
pages= 4689–4694|
|first10=Federico D.
year=2009|
|last11=Salmon
pmid=19258456|
|first11=John K.
issue=12|
|last12=Shan
pmc=2650503
|first12=Yibing
}}</ref><ref>{{cite journal|
|last13=Shaw
publisher=[[PNAS]]|author1=Yibing Shan |author2=Markus A. Seeliger |author3=Michael P. Eastwood |author4=Filipp Frank |author5=Huafeng Xu |author6=Morten Ø. Jensen |author7=Ron O. Dror |author8=John Kuriyan |author9=David E. Shaw |
|first13=David E.
title=A Conserved Protonation-Dependent Switch Controls Drug Binding in the Abl Kinase|
|access-date=2009-01-16
url=http://www.pnas.org/content/106/1/139.full|
|archive-date=2008-08-28
doi=10.1073/pnas.0811223106|
|archive-url=https://web.archive.org/web/20080828224042/http://sc06.supercomputing.org/schedule/pdf/pap259.pdf
journal=Proceedings of the National Academy of Sciences of the United States of America|
|url-status=dead
volume=106|
}}</ref><ref>
pages=139–144|
{{cite journal
year=2009|
|bibcode=2010PNAS..107.5833J
pmid=19109437|
|doi=10.1073/pnas.0911691107
issue=1|
pmc=2610013
|pmc=2851896
|pmid=20231479
}}</ref> The code uses novel parallel algorithms<ref>{{cite journal|
|title=Principles of conduction and hydrophobic gating in K+ channels
publisher=[[J. Chem. Phys.]]|author1=Kevin J. Bowers |author2=Ron O. Dror |author3=David E. Shaw |
|journal=Proceedings of the National Academy of Sciences
title=The Midpoint Method for Parallelization of Particle Simulations|
|volume=107 |issue=13 |pages=5833–5838
url=http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=JCPSA6000124000018184109000001&idtype=cvips&gifs=yes|
|year=2010
doi=10.1063/1.2191489|
|last1=Jensen |first1=M. O.
journal=Journal of Chemical Physics|
|last2=Borhani |first2=D. W.
volume=124|
|last3=Lindorff-Larsen |first3=K.
pages=184109:1–11|
|last4=Maragakis |first4=P.
year=2006|
|last5=Jogini |first5=V.
pmid=16709099|
|last6=Eastwood |first6=M. P.
issue=18
|last7=Dror |first7=R. O.
}}</ref> and numerical methods<ref>{{cite journal|
|last8=Shaw |first8=D. E.
publisher=[[J. Chem. Phys.]]|author1=Ross A. Lippert |author2=Kevin J. Bowers |author3=Ron O. Dror |author4=Michael P. Eastwood |author5=Brent A. Gregersen |author6=John L. Klepeis |author7=István Kolossváry |author8=David E. Shaw |
|doi-access=free
title=A Common, Avoidable Source of Error in Molecular Dynamics Integrators|
}}</ref><ref>
url=http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=JCPSA6000126000004046101000001&idtype=cvips&gifs=yes|
{{cite journal
doi=10.1063/1.2431176|
|doi=10.1073/pnas.0811065106
journal=Journal of Chemical Physics|
|pmid=19258456
volume=126|
|pmc=2650503
pages=046101:1–2|
|title=Identification of two distinct inactive conformations of the 2-adrenergic receptor reconciles structural and biochemical observations
year=2007|
|journal=Proceedings of the National Academy of Sciences
pmid=17286520|
|volume=106 |issue=12 |pages=4689–4694
issue=4
|year=2009
}}</ref> to achieve high performance on platforms containing a large number of processors,<ref>{{cite journal |author1=Edmond Chow |author2=Charles A. Rendleman |author3=Kevin J. Bowers |author4=Ron O. Dror |author5=Douglas H. Hughes |author6=Justin Gullingsrud |author7=Federico D. Sacerdoti |author8=David E. Shaw |title=Desmond Performance on a Cluster of Multicore Processors |url=http://deshawresearch.com/publications.html |publisher=D. E. Shaw Research Technical Report DESRES/TR--2008-01, July 2008 |year=2008}}</ref> but may also be executed on a single computer.
|last1=Dror |first1=R. O.
|last2=Arlow |first2=D. H.
|last3=Borhani |first3=D. W.
|last4=Jensen |first4=M. O.
|last5=Piana |first5=S.
|last6=Shaw |first6=D. E. |bibcode=2009PNAS..106.4689D
|doi-access=free
}}</ref><ref>
{{cite journal
|bibcode=2009PNAS..106..139S
|doi=10.1073/pnas.0811223106
|pmc=2610013
|pmid=19109437
|title=A conserved protonation-dependent switch controls drug binding in the Abl kinase
|journal=Proceedings of the National Academy of Sciences
|volume=106 |issue=1 |pages=139–144
|year=2009
|last1=Shan |first1=Y.
|last2=Seeliger |first2=M. A.
|last3=Eastwood |first3=M. P.
|last4=Frank |first4=F.
|last5=Xu |first5=H.
|last6=Jensen |first6=M. O.
|last7=Dror |first7=R. O.
|last8=Kuriyan |first8=J.
|last9=Shaw |first9=D. E.
|doi-access=free
}}</ref> The code uses novel parallel algorithms<ref>
{{cite journal
|doi=10.1063/1.2191489
|pmid=16709099
|bibcode=2006JChPh.124r4109B
|title=The midpoint method for parallelization of particle simulations
|journal=The Journal of Chemical Physics
|volume=124 |issue=18 |pages=184109
|year=2006
|last1=Bowers |first1=Kevin J.
|last2=Dror |first2=Ron O.
|last3=Shaw |first3=David E.
|doi-access=free
}}</ref> and numerical methods<ref>
{{cite journal
|doi=10.1063/1.2431176
|pmid=17286520
|bibcode=2007JChPh.126d6101L
|title=A common, avoidable source of error in molecular dynamics integrators
|journal=The Journal of Chemical Physics
|volume=126 |issue=4 |pages=046101
|year=2007
|last1=Lippert |first1=Ross A.
|last2=Bowers |first2=Kevin J.
|last3=Dror |first3=Ron O.
|last4=Eastwood |first4=Michael P.
|last5=Gregersen |first5=Brent A.
|last6=Klepeis |first6=John L.
|last7=Kolossvary |first7=Istvan
|last8=Shaw |first8=David E.
|s2cid=38661350
|doi-access=free
}}</ref> to achieve high performance on platforms containing multiple processors,<ref>
{{cite journal
|author1=Edmond Chow
|author2=Charles A. Rendleman
|author3=Kevin J. Bowers
|author4=Ron O. Dror
|author5=Douglas H. Hughes
|author6=Justin Gullingsrud
|author7=Federico D. Sacerdoti
|author8=David E. Shaw
|date=July 2008
|title=Desmond Performance on a Cluster of Multicore Processors
|url=http://deshawresearch.com/publications.html
|publisher=D. E. Shaw Research Technical Report DESRES/TR--2008-01
}}</ref> but may also be executed on a single computer.


The core and [[source code]] are available at no cost for non-commercial use by universities and other not-for-profit research institutions, and have been used in the [[Folding@home]] distributed computing project. Desmond is available as [[commercial software]] through [[Schrödinger (company)|Schrödinger, Inc.]]
The core and [[source code]] are available at no cost for non-commercial use by universities and other not-for-profit research institutions, and have been used in the [[Folding@home]] distributed computing project. Desmond is available as [[commercial software]] through [[Schrödinger (company)|Schrödinger, Inc.]]


== Molecular dynamics program ==
==Molecular dynamics program==


Desmond supports algorithms typically used to perform fast and accurate molecular dynamics. Long-range electrostatic energy and forces can be calculated using [[Ewald summation#Particle mesh Ewald (PME) method|particle mesh Ewald]]-based methods.<ref>{{cite journal
Desmond supports algorithms typically used to perform fast and accurate molecular dynamics. Long-range electrostatic energy and forces can be calculated using [[Ewald summation#Particle mesh Ewald (PME) method|particle mesh Ewald]]-based methods.<ref>
{{cite journal
|doi=10.1109/TSP.2009.2035984
|publisher=[[IEEE]]
|bibcode=2010ITSP...58.1122B
|author1=Kevin J. Bowers |author2=Ross A. Lippert |author3=Ron O. Dror |author4=David E. Shaw |title=Improved Twiddle Access for Fast Fourier Transforms
|title=Improved Twiddle Access for Fast Fourier Transforms
|url=http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=5313934&tag=1
|doi=10.1109/TSP.2009.2035984
|journal=IEEE Transactions on Signal Processing
|journal=IEEE Transactions on Signal Processing
|volume=58
|volume=58
Line 96: Line 171:
|pages=1122–1130
|pages=1122–1130
|year=2010
|year=2010
|last1=Bowers
}}</ref><ref>{{cite journal
|first1=K.J.
|publisher=[[J. Chem. Phys.]]
|last2=Lippert
|author1=Yibing Shan |author2=John L. Klepeis |author3=Michael P. Eastwood |author4=Ron O. Dror |author5=David E. Shaw |title=Gaussian Split Ewald: A Fast Ewald Mesh Method for Molecular Simulation
|first2=R.A.
|url=http://jcp.aip.org/jcpsa6/v122/i5/p054101_s1
|last3=Dror
|doi=10.1063/1.1839571
|first3=R.O.
|journal=Journal of Chemical Physics
|last4=Shaw
|volume=122
|first4=D.E.
|pages=054101:1–13
|s2cid=17240443
|year=2005
}}</ref><ref>
|pmid=15740304
{{cite journal
|issue=5
|doi=10.1063/1.1839571
}}</ref> Constraints can be enforced using the [[M-SHAKE#The M-SHAKE algorithm|M-SHAKE]] algorithm. These methods can be used together with time-scale splitting (RESPA-based) integration schemes.
|pmid=15740304
|bibcode=2005JChPh.122e4101S
|title=Gaussian split Ewald: A fast Ewald mesh method for molecular simulation
|journal=The Journal of Chemical Physics
|volume=122
|issue=5
|pages=054101
|year=2005
|last1=Shan
|first1=Yibing
|last2=Klepeis
|first2=John L.
|last3=Eastwood
|first3=Michael P.
|last4=Dror
|first4=Ron O.
|last5=Shaw
|first5=David E.
|s2cid=35865319
}}</ref> Constraints can be enforced using the [[M-SHAKE#The M-SHAKE algorithm|M-SHAKE]] algorithm. These methods can be used together with time-scale splitting (RESPA-based) integration schemes.


Desmond can compute energies and forces<ref>
Desmond can compute energies and forces<ref>{{cite journal |author1=Kresten Lindorff-Larsen |author2=Stefano Piana |author3=Kim Palmo |author4=Paul Maragakis |author5=John L. Klepeis |author6=Ron O. Dror |author7=David E. Shaw |title=Improved Side-Chain Torsion Potentials for the Amber ff99SB Protein Force Field
{{cite journal
|url=http://www3.interscience.wiley.com/journal/123314867/abstract?CRETRY=1&SRETRY=0
|doi=10.1002/prot.22711
|doi=10.1002/prot.22711
|pmc=2970904
|journal=Proteins: Structure, Function, and Bioinformatics
|pmid=20408171
|volume=78
|title=Improved side-chain torsion potentials for the Amber ff99SB protein force field
|pmc=2970904
|journal=Proteins: Structure, Function, and Bioinformatics
|pages=1950–1958
|volume=78
|year=2010
|issue=8
|pmid=20408171
|pages=1950–8
|issue=8
|year=2010
}}</ref> for many standard fixed-charged [[Force field (chemistry)|force fields]] used in biomolecular simulations, and is also compatible with polarizable force fields based on the [[Drude model|Drude]] formalism. A variety of integrators and support for various ensembles have been implemented in the code, including methods for temperature control (Andersen, [[Nosé-Hoover thermostat|Nosé-Hoover]], and [[Langevin dynamics|Langevin]]) and pressure control ([[Berendsen thermostat|Berendsen]], Martyna-Tobias-Klein, and Langevin). The code also supports methods for restraining atomic positions and molecular configurations; allows simulations to be carried out using a variety of periodic cell configurations; and has facilities for accurate checkpointing and restart.
|last1=Lindorff-Larsen
|first1=Kresten
|last2=Piana
|first2=Stefano
|last3=Palmo
|first3=Kim
|last4=Maragakis
|first4=Paul
|last5=Klepeis
|first5=John L.
|last6=Dror
|first6=Ron O.
|last7=Shaw
|first7=David E.
}}</ref> for many standard fixed-charged [[Force field (chemistry)|force fields]] used in biomolecular simulations, and is also compatible with polarizable force fields based on the [[Drude model|Drude]] formalism. A variety of integrators and support for various ensembles have been implemented in the code, including methods for temperature control ([[Andersen thermostat]], [[Nosé-Hoover thermostat|Nosé-Hoover]], and [[Langevin dynamics|Langevin]]) and pressure control ([[Berendsen thermostat|Berendsen]], [[Martyna-Tobias-Klein barostat|Martyna-Tobias-Klein]], and Langevin). The code also supports methods for restraining atomic positions and molecular configurations; allows simulations to be carried out using a variety of periodic cell configurations; and has facilities for accurate checkpointing and restart.


Desmond can also be used to perform absolute and relative free energy calculations (e.g., [[free energy perturbation]]). Other simulation methods (such as [[Parallel tempering|replica exchange]]) are supported through a plug-in-based infrastructure, which also allows users to develop their own simulation algorithms and models.
Desmond can also be used to perform absolute and relative free energy calculations (e.g., [[free energy perturbation]]). Other simulation methods (such as [[Parallel tempering|replica exchange]]) are supported through a plug-in-based infrastructure, which also allows users to develop their own simulation algorithms and models.


Desmond is also available in a [[graphics processing unit]] (GPU) accelerated version that is about 60-80 times faster than the [[central processing unit]] (CPU) version.
Desmond is also available in a [[graphics processing unit]] (GPU) accelerated version that is about 60-80 times faster than the [[central processing unit]] (CPU) version.


== Related software tools ==
==Related software tools==


Along with the molecular dynamics program, the Desmond software also includes tools for minimizing and energy analysis, both of which can be run efficiently in a parallel environment.
Along with the molecular dynamics program, the Desmond software also includes tools for minimizing and energy analysis, both of which can be run efficiently in a parallel environment.


Force fields parameters can be assigned using a template-based parameter assignment tool called Viparr. It currently supports several versions of the [[CHARMM#CHARMM force fields|CHARMM]], [[AMBER#Force field|Amber]] and [[OPLS]] force fields, and a range of different [[water model]]s.
Force fields parameters can be assigned using a template-based parameter assignment tool called [[Viparr]].<ref>{{cite web | url=https://github.com/DEShawResearch/viparr | title=DEShawResearch/Viparr | website=[[GitHub]] }}</ref> It currently supports several versions of the [[CHARMM#CHARMM force fields|CHARMM]], [[AMBER#Force field|Amber]] and [[OPLS]] force fields, and a range of different [[water model]]s.


Desmond is integrated with a molecular modeling environment (Maestro, developed by [[Schrödinger (company)|Schrödinger, Inc.]]) for setting up simulations of biological and chemical systems, and is compatible with [[Visual Molecular Dynamics]] (VMD) for trajectory viewing and analysis.
Desmond is integrated with a molecular modeling environment ([[Schrödinger Maestro|Maestro]], developed by [[Schrödinger (company)|Schrödinger, Inc.]]) for setting up simulations of biological and chemical systems, and is compatible with [[Visual Molecular Dynamics]] (VMD) for trajectory viewing and analysis.


== See also ==
==See also==

* [[D. E. Shaw Research]]
* [[Folding@home]]
* [[Comparison of software for molecular mechanics modeling]]
* [[Comparison of software for molecular mechanics modeling]]
* [[Metadynamics]]
* [[Molecular design software]]
* [[Molecular dynamics]]


==References==
==References==

{{Reflist}}
{{Reflist}}


== External links ==
==External links==
*{{Official website|deshawresearch.com}}
*{{Official website|deshawresearch.com}}
*[https://groups.google.com/group/desmond-md-users?lnk=srg&hl=en Desmond Users Group]
*[https://groups.google.com/group/desmond-md-users?lnk=srg&hl=en Desmond Users Group] (deleted)
*[http://www.schrodinger.com/productpage/14/3/ Schrödinger Desmond Product Page]
*[http://www.schrodinger.com/desmond Schrödinger Desmond Product Page]

{{Chemistry software}}


[[Category:Molecular dynamics software]]
[[Category:Molecular dynamics software]]
[[Category:Force fields]]
[[Category:Force fields (chemistry)]]

Latest revision as of 08:45, 21 August 2024

Desmond
Developer(s)D. E. Shaw Research
Operating systemLinux
Platformx86, x86-64, computer clusters
Available inEnglish
TypeComputational chemistry
LicenseProprietary freeware, commercial software
Websitewww.deshawresearch.com/resources_desmond.html, schrodinger.com/desmond

Desmond is a software package developed at D. E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems on conventional computer clusters.[1][2][3][4] The code uses novel parallel algorithms[5] and numerical methods[6] to achieve high performance on platforms containing multiple processors,[7] but may also be executed on a single computer.

The core and source code are available at no cost for non-commercial use by universities and other not-for-profit research institutions, and have been used in the Folding@home distributed computing project. Desmond is available as commercial software through Schrödinger, Inc.

Molecular dynamics program

[edit]

Desmond supports algorithms typically used to perform fast and accurate molecular dynamics. Long-range electrostatic energy and forces can be calculated using particle mesh Ewald-based methods.[8][9] Constraints can be enforced using the M-SHAKE algorithm. These methods can be used together with time-scale splitting (RESPA-based) integration schemes.

Desmond can compute energies and forces[10] for many standard fixed-charged force fields used in biomolecular simulations, and is also compatible with polarizable force fields based on the Drude formalism. A variety of integrators and support for various ensembles have been implemented in the code, including methods for temperature control (Andersen thermostat, Nosé-Hoover, and Langevin) and pressure control (Berendsen, Martyna-Tobias-Klein, and Langevin). The code also supports methods for restraining atomic positions and molecular configurations; allows simulations to be carried out using a variety of periodic cell configurations; and has facilities for accurate checkpointing and restart.

Desmond can also be used to perform absolute and relative free energy calculations (e.g., free energy perturbation). Other simulation methods (such as replica exchange) are supported through a plug-in-based infrastructure, which also allows users to develop their own simulation algorithms and models.

Desmond is also available in a graphics processing unit (GPU) accelerated version that is about 60-80 times faster than the central processing unit (CPU) version.

[edit]

Along with the molecular dynamics program, the Desmond software also includes tools for minimizing and energy analysis, both of which can be run efficiently in a parallel environment.

Force fields parameters can be assigned using a template-based parameter assignment tool called Viparr.[11] It currently supports several versions of the CHARMM, Amber and OPLS force fields, and a range of different water models.

Desmond is integrated with a molecular modeling environment (Maestro, developed by Schrödinger, Inc.) for setting up simulations of biological and chemical systems, and is compatible with Visual Molecular Dynamics (VMD) for trajectory viewing and analysis.

See also

[edit]

References

[edit]
  1. ^ Bowers, Kevin J.; Chow, Edmond; Xu, Huafeng; Dror, Ron O.; Eastwood, Michael P.; Gregersen, Brent A.; Klepeis, John L.; Kolossvary, Istvan; Moraes, Mark A.; Sacerdoti, Federico D.; Salmon, John K.; Shan, Yibing; Shaw, David E. (2006). "Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters" (PDF). ACM/IEEE SC 2006 Conference (SC'06). p. 43. doi:10.1109/SC.2006.54. ISBN 978-0-7695-2700-0. Archived from the original (PDF) on 2008-08-28. Retrieved 2009-01-16.
  2. ^ Jensen, M. O.; Borhani, D. W.; Lindorff-Larsen, K.; Maragakis, P.; Jogini, V.; Eastwood, M. P.; Dror, R. O.; Shaw, D. E. (2010). "Principles of conduction and hydrophobic gating in K+ channels". Proceedings of the National Academy of Sciences. 107 (13): 5833–5838. Bibcode:2010PNAS..107.5833J. doi:10.1073/pnas.0911691107. PMC 2851896. PMID 20231479.
  3. ^ Dror, R. O.; Arlow, D. H.; Borhani, D. W.; Jensen, M. O.; Piana, S.; Shaw, D. E. (2009). "Identification of two distinct inactive conformations of the 2-adrenergic receptor reconciles structural and biochemical observations". Proceedings of the National Academy of Sciences. 106 (12): 4689–4694. Bibcode:2009PNAS..106.4689D. doi:10.1073/pnas.0811065106. PMC 2650503. PMID 19258456.
  4. ^ Shan, Y.; Seeliger, M. A.; Eastwood, M. P.; Frank, F.; Xu, H.; Jensen, M. O.; Dror, R. O.; Kuriyan, J.; Shaw, D. E. (2009). "A conserved protonation-dependent switch controls drug binding in the Abl kinase". Proceedings of the National Academy of Sciences. 106 (1): 139–144. Bibcode:2009PNAS..106..139S. doi:10.1073/pnas.0811223106. PMC 2610013. PMID 19109437.
  5. ^ Bowers, Kevin J.; Dror, Ron O.; Shaw, David E. (2006). "The midpoint method for parallelization of particle simulations". The Journal of Chemical Physics. 124 (18): 184109. Bibcode:2006JChPh.124r4109B. doi:10.1063/1.2191489. PMID 16709099.
  6. ^ Lippert, Ross A.; Bowers, Kevin J.; Dror, Ron O.; Eastwood, Michael P.; Gregersen, Brent A.; Klepeis, John L.; Kolossvary, Istvan; Shaw, David E. (2007). "A common, avoidable source of error in molecular dynamics integrators". The Journal of Chemical Physics. 126 (4): 046101. Bibcode:2007JChPh.126d6101L. doi:10.1063/1.2431176. PMID 17286520. S2CID 38661350.
  7. ^ Edmond Chow; Charles A. Rendleman; Kevin J. Bowers; Ron O. Dror; Douglas H. Hughes; Justin Gullingsrud; Federico D. Sacerdoti; David E. Shaw (July 2008). "Desmond Performance on a Cluster of Multicore Processors". D. E. Shaw Research Technical Report DESRES/TR--2008-01. {{cite journal}}: Cite journal requires |journal= (help)
  8. ^ Bowers, K.J.; Lippert, R.A.; Dror, R.O.; Shaw, D.E. (2010). "Improved Twiddle Access for Fast Fourier Transforms". IEEE Transactions on Signal Processing. 58 (3): 1122–1130. Bibcode:2010ITSP...58.1122B. doi:10.1109/TSP.2009.2035984. S2CID 17240443.
  9. ^ Shan, Yibing; Klepeis, John L.; Eastwood, Michael P.; Dror, Ron O.; Shaw, David E. (2005). "Gaussian split Ewald: A fast Ewald mesh method for molecular simulation". The Journal of Chemical Physics. 122 (5): 054101. Bibcode:2005JChPh.122e4101S. doi:10.1063/1.1839571. PMID 15740304. S2CID 35865319.
  10. ^ Lindorff-Larsen, Kresten; Piana, Stefano; Palmo, Kim; Maragakis, Paul; Klepeis, John L.; Dror, Ron O.; Shaw, David E. (2010). "Improved side-chain torsion potentials for the Amber ff99SB protein force field". Proteins: Structure, Function, and Bioinformatics. 78 (8): 1950–8. doi:10.1002/prot.22711. PMC 2970904. PMID 20408171.
  11. ^ "DEShawResearch/Viparr". GitHub.
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