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Protocols

Desmond specifications

Information


Unique identifier OMICS_18936
Name Desmond
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Medium
Stability Stable
Maintained Yes

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No version available

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Maintainer


  • person_outline QikProp Team

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Desmond citations

 (14)
library_books

Adverse drug reactions triggered by the common HLA B*57:01 variant: virtual screening of DrugBank using 3D molecular docking

2018
J Cheminform
PMCID: 5790764
PMID: 29383457
DOI: 10.1186/s13321-018-0257-z

[…] olecular dynamic simulations with additional peptides and drug combinations are currently underway and will be discussed in a later publication. All molecular dynamic simulations were performed using Desmond as implemented in the Schrödinger Suite [–]. Systems were prepared in 10 × 10 × 10 Å buffered cubic box with a TIP3P solvent model. NPT simulations at 300 K were then performed with an OPLS3 f […]

call_split

Effects of Distal Mutations on the Structure, Dynamics and Catalysis of Human Monoacylglycerol Lipase

2018
Sci Rep
PMCID: 5789057
PMID: 29379013
DOI: 10.1038/s41598-017-19135-7
call_split See protocol

[…] Desmond, program in Schrodinger 2015–3 with OPLS3 force field was applied to build an aqueous biological system, followed by MD simulation. The SPC model was used to simulate water molecules,. The ort […]

call_split

Peptidomimetic blockade of MYB in acute myeloid leukemia

2018
Nat Commun
PMCID: 5760651
PMID: 29317678
DOI: 10.1038/s41467-017-02618-6
call_split See protocol

[…] with Simulaid program using the NMR structure of protein–peptide complex and converting C-MYB peptide from l-amino acids to d-amino acids in the presence of CBP. Simulations were performed using the Desmond molecular dynamics program. The starting structures were solvated with 6615 and 6714 SPC water molecules, respectively, with a 5 Å buffer of water in a rectangular box. Three chloride ions wer […]

library_books

Origin and evolution of transporter substrate specificity within the NPF family

2017
eLife
PMCID: 5336358
PMID: 28257001
DOI: 10.7554/eLife.19466.033

[…] buffer. Each system was subjected to a conjugate gradient energy minimization and relaxed by short molecular dynamics simulations (MDs) using the default ‘Relax model system’ protocol implemented in Desmond () followed by 20 ns of MDs with periodic boundary conditions. A restriction was applied to the secondary structure of the transporters using a spring constant force of 0.5 kcal × mol−1 × Å−2. […]

library_books

Early onset epileptic encephalopathy caused by a reduced sensitivity of Kv7.2 potassium channels to phosphatidylinositol 4,5 bisphosphate

2016
Sci Rep
PMCID: 5131271
PMID: 27905566
DOI: 10.1038/srep38167

[…] Software (https://www.schrodinger.com/prime). Molecular Dynamics simulations. The stability of the best scoring PIP2/Kv7.2 complex was further investigated by Molecular Dynamic (MD) simulations using Desmond MD system (https://www.schrodinger.com/desmond). The simulated environment was built using the system builder utility, with the structures being neutralized by Na+ and Cl− ions, which were add […]

library_books

Pharmacophore feature based virtual screening for finding potent GSK 3 inhibitors using molecular docking and dynamics simulations

2016
Bioinformation
PMCID: 5320924
PMID: 28293069
DOI: 10.6026/97320630012391

[…] as the docking engine in ArgusLab. Following the default protocol, the details of which can be found in previous studies, [] each molecular dynamics (MD) simulation was conducted for 20-ns using the Desmond module v3.6 [] from Schrodinger, Inc. For a brief period, the OPLS2005 force field [] was used to simulate the predefined three-site transferable intermolecular potential (TIP3P) water model [ […]


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