Desmond (software)

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.

  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)