VMD - Visual Molecular Dynamics

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code.
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Spotlight

The cells of higher organisms store their genetic material, the genome, in the so-called nucleus where they organize transcription of DNA into messenger-RNA, the blueprint for proteins. The messenger-RNA leaves the cell to be decoded by ribosomes that synthesize the respective proteins. Transcription factors, also proteins, control in the nucleus which parts of the cells' genomes are transcribed. Naturally, the access to the nucleus as well as exit from it must be restricted to transcription factors and related biomolecules. This is achieved by the nuclear pores, wide channels lined with brushes of polymers. The polymers are disordered proteins and prevent passage for most cellular proteins, except for so-called transport factors which bus transcription factors, messenger RNA, and certain larger biomolecule into and out of the nucleus. How transport factors are permitted to pass the nuclear pores, despite many studies, has been largely unknown. Molecular dynamics simulations, based on relevant crystallographic structures, using NAMD provided a comprehensive picture on the passage mechanism as reported recently. The simulations, analyzed with VMD, revealed that transport factors are dotted rather regularly on their surface with spots that bind to the brushes of nuclear pore proteins. While any protein may accidentally exhibit such a binding spot or two, only transport factors offer a regular pattern of such spots on their surface that apparently is their passport permitting them movement into and out of the nucleus, i.e., helping them to glide through the pores' protein brushes. More on simulations of transport factors can be found here.
Other Spotlights
Cse1p

image size:
movie: 4.6MB
made with VMD

Overview

Molecular representations
Supported molecular file formats
GPU-accelerated computing
Interactive molecular dynamics
Required software
Programs that use VMD
VMD research publications
How to cite VMD, Papers citing VMD

Download

Download (all versions)
VMD 1.8.7 (MacOS X, Unix, Windows)
VMD 1.8.6 (MacOS X, Unix, Windows)
VMD plugin library
VMD script library
License, Copyright and Disclaimer

Documentation and Support

User and installation guides
Quick help
FAQ
VMD-L mailing list
Bug List

News and Announcements

VMD and NAMD CUDA/OpenCL talks at SC2009 part of Parallel@Illinois
Investigating Interfaces of Macro-Molecular Complexes with Intervor
Probing Biomolecular Machines with Graphics Processors, CACM, 2009.
VMD QuicktimeVR/Flash rendering of PDB structures
VMD 1.8.7 released for MacOS X, Unix, and Windows (August 2009)
Visualisation of Cyclic and Multi-Branched Molecules with VMD, JMGM, 2009
VMD/Tachyon ambient occlusion lighting tutorial updated for VMD 1.8.7 (June 2009)
Outline shading tutorial updated for VMD 1.8.7 (June 2009)
High performance computation and interactive display of molecular orbitals on GPUs and multi-core CPUs, ACM GPGPU-2, 2009
Multilevel summation of electrostatic potentials using graphics processing units, Journal of Parallel Computing, 2009
2009 VMD Calendar
J. Comp. Chemistry cover image made with VMD
GPU-accelerated molecular modeling paper, J. Comp. Chem, 28:2618-2640, 2007
Create 3-D PDFs with VMD and Acrobat3D (Feb 2007)
VMD Images and Movies Tutorial (Jan 2007)
Past announcements

Gallery

Gallery of Posters, Images, and Movies made with VMD
Events and tutorial picture gallery

Development

VMD User Survey Results
VMD development status and pre-release test downloads
CVS source code access
VMD Programmer's documentation

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