VMD: visual molecular dynamics.
By W. Humphrey, A. Dalke, Klaus Schulten. 1996
Subfields: Computational Biology & Bioinformatics, Computational Chemistry & Drug Discovery
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In Computational Biology & Bioinformatics
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- Martin Weigt
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- José N. Onuchic
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In Computational Chemistry & Drug Discovery
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Citations in the corpus
- Molecular Docking and Structure-Based Drug Design Strategies (2015, neutral): “Program UCSF Chimera [193,194] VMD [195,196] Pymol [197,198] BALL [199,200] RasMol [201,202] Jmol [203] JSmol [204]”
- Graphene microsheets enter cells through spontaneous membrane penetration at edge asperities and corner sites (2013, methodology): “Because the lipid membranes generated by the membrane plug-in of VMD were far from the equilibrium state, an equilibrium run of 0.5 ns was carried out in which everything except lipid tails was fixed.”
- First-principles investigation of mechanical properties of silicene, germanene and stanene (2017, methodology): “VMD [43] software is used to illustrate these structures.”
- Wear mechanism of diamond tools against single crystal silicon in single point diamond turning process (2013, unknown): “A piece of code known as Visual Molecular Dynamics (VMD) [51] was used for this purpose.”
- VAMPnets for deep learning of molecular kinetics (2017, background): “The first step of a typical processing pipeline is fea-turization, where the MD coordinates are either aligned (removing translation and rotation of the molecule of interest) or transformed into internal coordinates such as residue distances, contact maps or torsion angles [4, 13, 15, 16].”
- Higher-Resolution Structure of the Human Insulin Receptor Ectodomain: Multi-Modal Inclusion of the Insert Domain (2016, methodology): “We thus extended the existing interactive molecular dynamics plugin autoIMD of the VMD package (Humphrey et al., 1996) to add MDFF functionality along with standard stereochemical restraints, then coupled it to a haptic interface (a Novint Falcon) to allow 3D interaction with real-time force feedbac”