VMD Spotlights
We are continually adding new features to VMD (and expanding the
spotlight to highlight more of the existing features of VMD)
so come back and visit often.
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VMD is capable of working with very large structures up to the limits
of available memory. The 64-bit versions of VMD allow large-size and
long-timescale simulation trajectories to be loaded into physical memory
and accommodate large volumetric datasets.
The 64 million atom HIV capsid simulation
described in the May 30, 2013 issue of Nature is a first-class
example of what can be done with VMD on an appropriately equipped
graphics workstation. The HIV-1 model was prepared for simulation
using the structure building tools and scripting features of VMD were
later used for trajectory analysis. The all-atom structure of the
HIV-1 capsid shown on the Nature cover was rendered within VMD
using the internal
Tachyon
ray tracing engine, and was then composited with an artistic
representation of the viral envelope and the Nature cover text.
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Human immunodeficiency virus type 1 (HIV-1) is the major cause of
AIDS, for which treatments need to be developed continuously as the
virus becomes quickly resistant to new drugs. When the virus infects
a human cell it releases into the cell its capsid, a closed, stable
container protecting the viral genetic material. However, interaction
with the cell triggers at some point an instability of the capsid,
leading to a well timed release of the genetic material that merges
then with the cell's genes and begins to control the cell. The dual
role of the capsid, to be functionally both stable and unstable, makes
it in principle an ideal target for antiviral drugs and, in fact,
treatments of other viral infections successfully target the
respective capsids. The size of the HIV-1 capsid (about 1,300
proteins), and its irregular shape had prevented so far the resolution
of a full capsid atomic-level structure. However, in a tour de force
effort, groups of experimental and computational scientists have now
resolved the capsid's chemical structure (deposited to the protein
data bank under the accession codes 3J3Q
and 3J3Y).
As reported
recently (see also journal cover), the
researchers combined NMR structure analysis, electron microscopy and
data-guided molecular dynamics
simulations utilizing VMD to prepare
and analyze simulations performed using NAMD on one of the most powerful computers
worldwide, Blue
Waters, to obtain and characterize the HIV-1 capsid. The
discovery can guide now the design of novel drugs for enhanced
antiviral therapy.
More information is available on our virus website, in video, and in a press release.
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See also movie: 15.5MB
made with VMD
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VMD is frequently used to make figures and illustrations that grace
the cover pages of textbooks and journals.
The cover image on the August 2008 issue of Science
by Klein and Shinoda demonstrates the use of VMD for visualization of large coarse-grain molecular dynamics trajectories.
The image illustrates a simulation of a vesicle interacting with a lipid bilayer, with
over 1 million coarse-grained interaction sites, equivalent to over 10 million atoms.
Read more about their work here.
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Since its inception, VMD was designed to take advantage of
graphics processing units (GPUs) for interactive renderings of large
biomolecular complexes. Recently, GPUs have become programmable and
their massive parallel processing capabilities can now be utilized
for non-graphical computations. VMD makes uses of this type GPU-based
parallel computation to greatly accelerate calculation of electrostatic
potential fields, used for visualization and analysis,
and for modeling operations such as ion placement.
Ongoing VMD development efforts will expand the use of GPU acceleration
even further, for acceleration of volumetric processing,
structure and trajectory analysis, and compute-limited operations
performed within VMD and it's plugins.
More information on GPU acceleration of molecular modeling
applications is provided
here.
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Globins are oxygen-storing proteins, vital to life. In our blood,
hemoglobins carry oxygen from our lungs to every cell in our body. In our
muscles, myoglobins keep reserves of oxygen to make sure it is available
when needed. In some plants, leghemoglobins capture oxygen molecules that
would otherwise be harmful to the production of ammonium necessary for the
plant's survival. All these globins possess an iron-containig "heme", that
grabs on to oxygen for a short time, and share the same protein
architecture, despite large variations in their sequences. Since the heme
group is buried inside a globin, scientists wondered how oxygen makes its
way inside the protein to reach it.
Exploring the motion and energetics of globins using the program NAMD researchers learned to gather data that
permitted them to visualize, utilizing the VMD software, all the pathways taken by oxygen
migrating inside whale myoglobin (see the Aug 2006 highlight and related
publication). However, when the researchers turned their attention to
the rest of the globin family to compute their oxygen pathways, they
found, on their computational spelunking trip,
something surprising. Given the conserved architecture of all globins,
they expected to see similar oxygen pathways throughout the globin family,
but they saw the opposite! Aside from a conserved pocket right at the
heme binding site, the distribution of oxygen pathways showed very little
similarity from one globin to the next. This result is described in a
recent report, which
shows that oxygen-pathways are not conserved by evolution, and that their
location is not determined by a protein's overall architecture, but rather
by its local amino acids. The researchers also learned which amino acids
are found more often than others lining oxygen pathways, recognizing that
bulky side groups are not hindering, but favoring oxygen passage. More
information can be found here.
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Modern computers include a massively parallel graphics
processing unit (GPU) designed to perform geometry and lighting
calculations at blistering speeds.
State of the art GPUs can perform 0.5 teraFLOPS with their
hundred cores.
The tremendous computational power of GPUs
was untapped by scientific computations because it could only be
accessed with difficulty until now.
As
reported in the Journal of Computational Chemistry, recent
advances
allowing GPUs to be used for general purpose computing have
boosted the performance of a number of molecular modeling applications,
including
NAMD
simulations and
VMD
electrostatic potential calculations.
The accelerated versions of these
applications run five to one hundred times faster than on the best
CPU-based hardware, allowing a single desktop computer equipped
with a GPU to provide processing power equivalent
to an entire, large computing cluster.
More information on GPU acceleration of molecular modeling
applications is provided
here.
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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. |
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image size:
movie: 4.6MB
made with VMD
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Because oxygen gas is very reactive, it is frequently employed by the cell
as a reagent by proteins called enzymes, which build the organic compounds
that the cell needs. One such enzyme belongs to the copper amine oxidase
family. These proteins transform amine-containing compounds into molecules
needed by the cell, by reacting the compounds with oxygen. Researchers
have long been interested in finding out how the various reagents reach
the buried copper active site before the final oxidation reaction can
occur. While copper amine oxidases exhibit an obvious channel for
capturing the amine compounds to be modified, it had been unclear until
now how oxygen molecules make their way through the enzyme. With the help
of computer simulations using NAMD,
researchers have identified in a recent publication, the
routes taken by oxygen inside various copper amine oxidases from different
species. In order to accomplish this, they analyzed simulations of the
motions of four copper amine oxidases, using the VMD analysis and visualization software, which
can predict the probability of finding oxygen molecules anywhere inside
the simulated proteins. This analysis found numerous oxygen conduction
routes inside each copper amine oxidase, i.e., oxygen can enter the
protein through many routes, as it would in a sponge. More information on
finding O2 migration pathways in proteins can be found here.
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The popular Adobe PDF document format (PDF version 1.6) now supports
inclusion of 3-D geometry. The latest versions of Adobe Acrobat Reader
can now display, rotate, and animate 3-D models embedded within these
PDF documents. This capabilities provide a tremendous new opportunity
for creating tutorials, presentations, and electronic textbooks containing
3-D models of biomolecules that can be interactively manipulated by
the reader. For more information, see the
short tutorial on creating 3-D PDF files with VMD
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The
Tachyon
parallel ray tracer included with VMD has been updated with
the ability to display molecules with ambient occlusion lighting.
This lighting technique mimicks some of the effects that occur under
conditions of omnidirectional diffuse illumination, e.g. outdoors on an
overcast day. This lighting used in concert with traditional point
source lights and directional lights to increase the perception of shape and
depth in images of molecular structures, and decreases the deleterious
effects of harsh shadows which otherwise occur with lighting based on
a small number of direct light sources. This lighting model is particularly
good at emulating the appearance of chalky materials, and can make
molecular graphics more understandable, not to mention aesthetically appealing.
A short
tutorial is available
on using these new lighting and shading features with VMD, along with a number
of representative example images.
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"I would add that VMD (and similar tools, if they yet exist) will
become a primary platform upon which to study a wide range of
biological problems in the future. VMD adds a new dimension to the
biologist's thinking. Certain thoughts generated in interaction with
VMD images are inconceivable otherwise; the `language' essential to
generating these ideas would just not be there! In other words, VMD
is far from a simple `visualization tool' for a biologist, it is a
true thinking tool. Without it a whole class of biological
hypotheses would simply not exist."
-- Carl Woese
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VMD supports user-defined material and shading properties that
can be used to render molecular graphics in a more illustrative
style. Future versions of VMD will expand on this capability
through increased use of programmable shading technology. This will
bring many molecular rendering features previously found only in batch mode
software renderers into the realm of interactive molecular visualization.
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VMD is capable of working with very large structures up to the limits
of available memory. The 64-bit versions of VMD allow huge simulation
trajectories to be loaded into physical memory and accomodate large
volumetric datasets.
This 1,000,000+ atom Satellite Tobacco Mosaic Virus simulation
is an example of the size simulation trajectory that one can analyze and
display with VMD on an appropriately equipped graphics workstation.
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VMD includes a plugin for creating and running
APBS electrostatics calculations
and can
display the resulting ouput
including potential maps, solvent accessibility maps,
and other data produced by the APBS job. Recent versions of VMD also have
the ability to run APBS jobs on remote clusters or supercomputers for fast
turnaround of high resolution potential calculation needed for visualization
and analysis.
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VMD can load and display volumetric data sets, including
electron density maps, electron orbitals, potential maps,
and various types of user-generated volumetric data.
The VMD plugin library
contains support for a large number of volumetric file formats.
Users can also import their own data file formats by writing
their own loader scripts using the "mol volume" command.
Volumetric data can be rendered using "VolumeSlice" or "Isosurface"
representations, each of which provides several geometric rendering
styles for viewing the data, varying isolevels, slice plane position,
etc.
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VMD includes a Virtual DNA Viewer
plugin which can be used to render images of chromatin using ideal DNA
interbasepair helical parameters (in proper r.h.s. ref. frame ordering).
This plugin is useful for investigating the folding of chromatin based on the
"two-angle" model where the total linker length and twist between nucleosomes
determines the overall geometry of chromatin. This is an example of the
type of visualizations that can be done with VMD using mathematical
models and equations rather than all-atom structure data.
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VMD can be used to
display the results
of HOLE calculations. HOLE
calculates pore dimensions of the holes through molecular structures of
ion channels. This is one of many examples of how third party packages
can make use of the visualization capabilties of VMD.
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Recent improvements to the data structures and algorithms used to
display and analyze molecular structures in VMD have improved
it's utility in
bionanotechnology,
and materials science where large structures, various types of non-biological
matter, and non-polymeric structural elements are often present.
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Dr. Oliver Beckstein's VMD image was voted "highly commended" in the
2005 Visions of Science Photographic Awards.
The image illustrates the nicotinic acetylcholine receptor.
The image was created by loading the crystal structure of the receptor and
water density on a 3D grid into VMD 1.8.3 and rendered with Raster3D 2.7c.
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VMD provides the ability to render molecular scenes using
external programs such as ray tracers and commercial
animation packages. This feature can be used to attain
higher image quality than is normally possible using the
built-in OpenGL rendering features in VMD.
The Tachyon parallel ray tracer is distributed with VMD.
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VMD can display solvent-exluded molecular surfaces through the use
of the program
MSMS.
MSMS provides VMD with fast surface calculation and display, and VMD
uses high-performance display algorithms to allow large or complex
surfaces to be drawn at interactive rates.
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VMD can now make movies easier than ever before, with the use of a
movie plugin
that takes care of the entire movie making process.
The vmdmovie plugin generates one of several built-in movie types, according
to user selectable options. Once preferences and selections are made, the
movie generator takes control of VMD and takes care of the entire
process, from the generation of individual movie frames using on-screen
snapshots or ray tracers, image format conversion staging of the image
data for compression, invocation of movie compressor programs, and
final disk space cleanup and temporary file deletion. This makes the
whole process of making movies much simpler for inexperienced users.
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VMD can load and display the results of ab initio simulations done
with packages such as CPMD, GAMESS, Gaussian, ESPRESSO/PWScf, and others.
An excellent tutorial on using VMD with these packages
is available here.
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VMD is capable of working with very large structures up to the limits
of available memory. The 64-bit versions of VMD allow huge simulation
trajectories to be loaded into physical memory and accomodate large
volumetric datasets. This 400,000 atom virus structure is just a simple
example of what can be done with VMD on an appropriately equipped
graphics workstation.
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VMD is frequently used to make figures and illustrations that grace
the cover pages of textbooks and journals. A sampling of some of the
VMD cover page images produced by local researchers and collaborators can be
viewed here.
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VMD includes a
Ramachandran plot plugin
which plots
Phi and Psi angles for a selected molecule. The angle plot
automatically updates when simulation trajectory frames
are advanced by hand, or when animated. Each plotted angle
is individually selectable, and reports its segment ID,
residue name, residue ID, Phi angle, and Psi angle, when selected.
Ramachandran plots can be saved to a postscript file for inclusion
into publications.
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VMD can be used with 3-D printers to create solid models of molecular
structures such as the LH-II
heterodimer unit shown at right. The most recent version of VMD supports
the newest color-capable 3-D printers, and can generate STL or VRML files
suitable for 3-D printing. Two identical LH-II heterodimer units were
printed in 6.4 hours on a Z-Corp Z400
3-D printer at an approximate cost of $1 to $2 per cubic inch.
Each of the two solid models consumed 12.4 cubic inches of the ZP102 powder.
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VMD provides user-editable "materials" which can be applied to
molecular geometry. These material properties control the
details of how VMD shades the molecular geometry, and how
transparent or opaque the displayed molecular geometry is.
With this feature, one can easily create nice looking transparent
surfaces which allow inner structural details to be seen within a
large molecular structure. The material controls can be particularly
helpful when rendering molecular scenes using external ray tracers,
each of which typically differ slightly.
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VMD provides a
sequence plugin
which can be used to view a structure's
sequence, secondary structure code, and B value in a scrolling window.
The sequence viewer can zoom in on a region of interest, and selections
can be made on the sequence, which are then highlighted on the structure
in VMD's OpenGL graphics window.
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VMD takes advantage of inexpensive game technologies, graphics boards and
stereo glasses to provide capabilities for PC users which were once
only available in $40,000 workstations. For only a few hundred dollars,
it is now possible to equip most desktop PC's with stereoscopic display
capabilities, hardware accelerated 3-D rendering, and six-degree-of-freedom
motion control capability.
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VMD supports the use of separate displays for its graphical user interface
forms and menus, and its 3-D graphics display window.
This allows VMD to be used easily in a
theatre or auditorium environment
where one display
channel may be projected on a large screen for classes or presentations,
and other screens are only seen by the presenter or helpers. This feature
lets the presenter show just the VMD graphics window on the projection
system, without distracting the audience with other user interfaces,
menus, etc.
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BioCoRE enhances VMD by making it very
easy to share molecular views with collaborators. Once you have a
desired view in VMD, the view can be saved back to BioCoRE by selecting
an option in a special BioCoRE window. Collaborators can then use
BioCoRE to load the same view in their own copy of VMD.
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VMD includes built-in support for
IMD (Interactive Molecular Dynamics)
simulations using NAMD, or Protomol.
IMD allows a researcher to interact with molecular structures within
a running simulation, applying forces on groups of atoms in the simulation.
The user experiences force feedback when resistance is encountered, through
the use of 3-D motion control devices with haptic feedback.
IMD techniques are currently being applied to studies of the
Glycerol channel.
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VMD includes built-in support for high-end quad-buffered
stereoscopic rendering which can be used in projection theatres
as well as desktop graphics workstations. Sterescopic display aids
significantly in the perception of three dimensional structures and
has been a key feature in VMD since its first release. VMD also
provides support for inexpensive game-oriented stereo glasses, and even
anaglyphic (Red/Blue) stereo.
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VMD can be used with tiled displays and cluster-based rendering
systems for relatively low-cost, high resolution display of
molecular geometry. This feature is particularly attractive for
institutions with tiled display systems used for auditoriums, or
other large-format presentation rooms. The image at the right
shows a six projector tiled display at
NCSA, running VMD.
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VMD supports the use of six-degree-of-freedom motion control devices
such as the Spaceball and Magellan. These input devices provide an
easy-to-use interface for performing complex 3-D manipulation, and
leave your other hand free to use the mouse and keyboard at the same
time. These devices can also be used to manipulate 3-D pointers
in the scene for meetings and presentations.
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VMD is capable of working with very large structures up to the limits
of available memory. The 64-bit versions of VMD allow large-size and
long-timescale simulation trajectories to be loaded into physical memory
and accommodate large volumetric datasets.
The 64 million atom HIV capsid simulation
described in the May 30, 2013 issue of Nature is a first-class
example of what can be done with VMD on an appropriately equipped
graphics workstation. The HIV-1 model was prepared for simulation
using the structure building tools and scripting features of VMD were
later used for trajectory analysis. The all-atom structure of the
HIV-1 capsid shown on the Nature cover was rendered within VMD
using the internal
Tachyon
ray tracing engine, and was then composited with an artistic
representation of the viral envelope and the Nature cover text.
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VMD is capable of working with very large structures up to the limits
of available memory. The 64-bit versions of VMD allow large-size and
long-timescale simulation trajectories to be loaded into physical memory
and accommodate large volumetric datasets.
The 64 million atom HIV capsid simulation
described in the May 30, 2013 issue of Nature is a first-class
example of what can be done with VMD on an appropriately equipped
graphics workstation. The HIV-1 model was prepared for simulation
using the structure building tools and scripting features of VMD were
later used for trajectory analysis. The all-atom structure of the
HIV-1 capsid shown on the Nature cover was rendered within VMD
using the internal
Tachyon
ray tracing engine, and was then composited with an artistic
representation of the viral envelope and the Nature cover text.
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VMD is capable of working with very large structures up to the limits
of available memory. The 64-bit versions of VMD allow large-size and
long-timescale simulation trajectories to be loaded into physical memory
and accommodate large volumetric datasets.
The 64 million atom HIV capsid simulation
described in the May 30, 2013 issue of Nature is a first-class
example of what can be done with VMD on an appropriately equipped
graphics workstation. The HIV-1 model was prepared for simulation
using the structure building tools and scripting features of VMD were
later used for trajectory analysis. The all-atom structure of the
HIV-1 capsid shown on the Nature cover was rendered within VMD
using the internal
Tachyon
ray tracing engine, and was then composited with an artistic
representation of the viral envelope and the Nature cover text.
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VMD is capable of working with very large structures up to the limits
of available memory. The 64-bit versions of VMD allow large-size and
long-timescale simulation trajectories to be loaded into physical memory
and accommodate large volumetric datasets.
The 64 million atom HIV capsid simulation
described in the May 30, 2013 issue of Nature is a first-class
example of what can be done with VMD on an appropriately equipped
graphics workstation. The HIV-1 model was prepared for simulation
using the structure building tools and scripting features of VMD were
later used for trajectory analysis. The all-atom structure of the
HIV-1 capsid shown on the Nature cover was rendered within VMD
using the internal
Tachyon
ray tracing engine, and was then composited with an artistic
representation of the viral envelope and the Nature cover text.
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VMD is capable of working with very large structures up to the limits
of available memory. The 64-bit versions of VMD allow large-size and
long-timescale simulation trajectories to be loaded into physical memory
and accommodate large volumetric datasets.
The 64 million atom HIV capsid simulation
described in the May 30, 2013 issue of Nature is a first-class
example of what can be done with VMD on an appropriately equipped
graphics workstation. The HIV-1 model was prepared for simulation
using the structure building tools and scripting features of VMD were
later used for trajectory analysis. The all-atom structure of the
HIV-1 capsid shown on the Nature cover was rendered within VMD
using the internal
Tachyon
ray tracing engine, and was then composited with an artistic
representation of the viral envelope and the Nature cover text.
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VMD is capable of working with very large structures up to the limits
of available memory. The 64-bit versions of VMD allow large-size and
long-timescale simulation trajectories to be loaded into physical memory
and accommodate large volumetric datasets.
The 64 million atom HIV capsid simulation
described in the May 30, 2013 issue of Nature is a first-class
example of what can be done with VMD on an appropriately equipped
graphics workstation. The HIV-1 model was prepared for simulation
using the structure building tools and scripting features of VMD were
later used for trajectory analysis. The all-atom structure of the
HIV-1 capsid shown on the Nature cover was rendered within VMD
using the internal
Tachyon
ray tracing engine, and was then composited with an artistic
representation of the viral envelope and the Nature cover text.
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VMD is capable of working with very large structures up to the limits
of available memory. The 64-bit versions of VMD allow large-size and
long-timescale simulation trajectories to be loaded into physical memory
and accommodate large volumetric datasets.
The 64 million atom HIV capsid simulation
described in the May 30, 2013 issue of Nature is a first-class
example of what can be done with VMD on an appropriately equipped
graphics workstation. The HIV-1 model was prepared for simulation
using the structure building tools and scripting features of VMD were
later used for trajectory analysis. The all-atom structure of the
HIV-1 capsid shown on the Nature cover was rendered within VMD
using the internal
Tachyon
ray tracing engine, and was then composited with an artistic
representation of the viral envelope and the Nature cover text.
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VMD is capable of working with very large structures up to the limits
of available memory. The 64-bit versions of VMD allow large-size and
long-timescale simulation trajectories to be loaded into physical memory
and accommodate large volumetric datasets.
The 64 million atom HIV capsid simulation
described in the May 30, 2013 issue of Nature is a first-class
example of what can be done with VMD on an appropriately equipped
graphics workstation. The HIV-1 model was prepared for simulation
using the structure building tools and scripting features of VMD were
later used for trajectory analysis. The all-atom structure of the
HIV-1 capsid shown on the Nature cover was rendered within VMD
using the internal
Tachyon
ray tracing engine, and was then composited with an artistic
representation of the viral envelope and the Nature cover text.
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VMD is capable of working with very large structures up to the limits
of available memory. The 64-bit versions of VMD allow large-size and
long-timescale simulation trajectories to be loaded into physical memory
and accommodate large volumetric datasets.
The 64 million atom HIV capsid simulation
described in the May 30, 2013 issue of Nature is a first-class
example of what can be done with VMD on an appropriately equipped
graphics workstation. The HIV-1 model was prepared for simulation
using the structure building tools and scripting features of VMD were
later used for trajectory analysis. The all-atom structure of the
HIV-1 capsid shown on the Nature cover was rendered within VMD
using the internal
Tachyon
ray tracing engine, and was then composited with an artistic
representation of the viral envelope and the Nature cover text.
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VMD is capable of working with very large structures up to the limits
of available memory. The 64-bit versions of VMD allow large-size and
long-timescale simulation trajectories to be loaded into physical memory
and accommodate large volumetric datasets.
The 64 million atom HIV capsid simulation
described in the May 30, 2013 issue of Nature is a first-class
example of what can be done with VMD on an appropriately equipped
graphics workstation. The HIV-1 model was prepared for simulation
using the structure building tools and scripting features of VMD were
later used for trajectory analysis. The all-atom structure of the
HIV-1 capsid shown on the Nature cover was rendered within VMD
using the internal
Tachyon
ray tracing engine, and was then composited with an artistic
representation of the viral envelope and the Nature cover text.
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VMD is capable of working with very large structures up to the limits
of available memory. The 64-bit versions of VMD allow large-size and
long-timescale simulation trajectories to be loaded into physical memory
and accommodate large volumetric datasets.
The 64 million atom HIV capsid simulation
described in the May 30, 2013 issue of Nature is a first-class
example of what can be done with VMD on an appropriately equipped
graphics workstation. The HIV-1 model was prepared for simulation
using the structure building tools and scripting features of VMD were
later used for trajectory analysis. The all-atom structure of the
HIV-1 capsid shown on the Nature cover was rendered within VMD
using the internal
Tachyon
ray tracing engine, and was then composited with an artistic
representation of the viral envelope and the Nature cover text.
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VMD is capable of working with very large structures up to the limits
of available memory. The 64-bit versions of VMD allow large-size and
long-timescale simulation trajectories to be loaded into physical memory
and accommodate large volumetric datasets.
The 64 million atom HIV capsid simulation
described in the May 30, 2013 issue of Nature is a first-class
example of what can be done with VMD on an appropriately equipped
graphics workstation. The HIV-1 model was prepared for simulation
using the structure building tools and scripting features of VMD were
later used for trajectory analysis. The all-atom structure of the
HIV-1 capsid shown on the Nature cover was rendered within VMD
using the internal
Tachyon
ray tracing engine, and was then composited with an artistic
representation of the viral envelope and the Nature cover text.
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VMD is capable of working with very large structures up to the limits
of available memory. The 64-bit versions of VMD allow large-size and
long-timescale simulation trajectories to be loaded into physical memory
and accommodate large volumetric datasets.
The 64 million atom HIV capsid simulation
described in the May 30, 2013 issue of Nature is a first-class
example of what can be done with VMD on an appropriately equipped
graphics workstation. The HIV-1 model was prepared for simulation
using the structure building tools and scripting features of VMD were
later used for trajectory analysis. The all-atom structure of the
HIV-1 capsid shown on the Nature cover was rendered within VMD
using the internal
Tachyon
ray tracing engine, and was then composited with an artistic
representation of the viral envelope and the Nature cover text.
|
|
|
|
VMD is capable of working with very large structures up to the limits
of available memory. The 64-bit versions of VMD allow large-size and
long-timescale simulation trajectories to be loaded into physical memory
and accommodate large volumetric datasets.
The 64 million atom HIV capsid simulation
described in the May 30, 2013 issue of Nature is a first-class
example of what can be done with VMD on an appropriately equipped
graphics workstation. The HIV-1 model was prepared for simulation
using the structure building tools and scripting features of VMD were
later used for trajectory analysis. The all-atom structure of the
HIV-1 capsid shown on the Nature cover was rendered within VMD
using the internal
Tachyon
ray tracing engine, and was then composited with an artistic
representation of the viral envelope and the Nature cover text.
|
|
|
|
VMD is capable of working with very large structures up to the limits
of available memory. The 64-bit versions of VMD allow large-size and
long-timescale simulation trajectories to be loaded into physical memory
and accommodate large volumetric datasets.
The 64 million atom HIV capsid simulation
described in the May 30, 2013 issue of Nature is a first-class
example of what can be done with VMD on an appropriately equipped
graphics workstation. The HIV-1 model was prepared for simulation
using the structure building tools and scripting features of VMD were
later used for trajectory analysis. The all-atom structure of the
HIV-1 capsid shown on the Nature cover was rendered within VMD
using the internal
Tachyon
ray tracing engine, and was then composited with an artistic
representation of the viral envelope and the Nature cover text.
|
|
|
|
VMD is capable of working with very large structures up to the limits
of available memory. The 64-bit versions of VMD allow large-size and
long-timescale simulation trajectories to be loaded into physical memory
and accommodate large volumetric datasets.
The 64 million atom HIV capsid simulation
described in the May 30, 2013 issue of Nature is a first-class
example of what can be done with VMD on an appropriately equipped
graphics workstation. The HIV-1 model was prepared for simulation
using the structure building tools and scripting features of VMD were
later used for trajectory analysis. The all-atom structure of the
HIV-1 capsid shown on the Nature cover was rendered within VMD
using the internal
Tachyon
ray tracing engine, and was then composited with an artistic
representation of the viral envelope and the Nature cover text.
|
|
|
|
VMD is capable of working with very large structures up to the limits
of available memory. The 64-bit versions of VMD allow large-size and
long-timescale simulation trajectories to be loaded into physical memory
and accommodate large volumetric datasets.
The 64 million atom HIV capsid simulation
described in the May 30, 2013 issue of Nature is a first-class
example of what can be done with VMD on an appropriately equipped
graphics workstation. The HIV-1 model was prepared for simulation
using the structure building tools and scripting features of VMD were
later used for trajectory analysis. The all-atom structure of the
HIV-1 capsid shown on the Nature cover was rendered within VMD
using the internal
Tachyon
ray tracing engine, and was then composited with an artistic
representation of the viral envelope and the Nature cover text.
|
|
|
|
VMD is capable of working with very large structures up to the limits
of available memory. The 64-bit versions of VMD allow large-size and
long-timescale simulation trajectories to be loaded into physical memory
and accommodate large volumetric datasets.
The 64 million atom HIV capsid simulation
described in the May 30, 2013 issue of Nature is a first-class
example of what can be done with VMD on an appropriately equipped
graphics workstation. The HIV-1 model was prepared for simulation
using the structure building tools and scripting features of VMD were
later used for trajectory analysis. The all-atom structure of the
HIV-1 capsid shown on the Nature cover was rendered within VMD
using the internal
Tachyon
ray tracing engine, and was then composited with an artistic
representation of the viral envelope and the Nature cover text.
|
|
|
|
VMD is capable of working with very large structures up to the limits
of available memory. The 64-bit versions of VMD allow large-size and
long-timescale simulation trajectories to be loaded into physical memory
and accommodate large volumetric datasets.
The 64 million atom HIV capsid simulation
described in the May 30, 2013 issue of Nature is a first-class
example of what can be done with VMD on an appropriately equipped
graphics workstation. The HIV-1 model was prepared for simulation
using the structure building tools and scripting features of VMD were
later used for trajectory analysis. The all-atom structure of the
HIV-1 capsid shown on the Nature cover was rendered within VMD
using the internal
Tachyon
ray tracing engine, and was then composited with an artistic
representation of the viral envelope and the Nature cover text.
|
|
|
|
Human immunodeficiency virus type 1 (HIV-1) is the major cause of
AIDS, for which treatments need to be developed continuously as the
virus becomes quickly resistant to new drugs. When the virus infects
a human cell it releases into the cell its capsid, a closed, stable
container protecting the viral genetic material. However, interaction
with the cell triggers at some point an instability of the capsid,
leading to a well timed release of the genetic material that merges
then with the cell's genes and begins to control the cell. The dual
role of the capsid, to be functionally both stable and unstable, makes
it in principle an ideal target for antiviral drugs and, in fact,
treatments of other viral infections successfully target the
respective capsids. The size of the HIV-1 capsid (about 1,300
proteins), and its irregular shape had prevented so far the resolution
of a full capsid atomic-level structure. However, in a tour de force
effort, groups of experimental and computational scientists have now
resolved the capsid's chemical structure (deposited to the protein
data bank under the accession codes 3J3Q
and 3J3Y).
As reported
recently (see also journal cover), the
researchers combined NMR structure analysis, electron microscopy and
data-guided molecular dynamics
simulations utilizing VMD to prepare
and analyze simulations performed using NAMD on one of the most powerful computers
worldwide, Blue
Waters, to obtain and characterize the HIV-1 capsid. The
discovery can guide now the design of novel drugs for enhanced
antiviral therapy.
More information is available on our virus website, in video, and in a press release.
|
|
See also movie: 15.5MB
made with VMD
|
|
Human immunodeficiency virus type 1 (HIV-1) is the major cause of
AIDS, for which treatments need to be developed continuously as the
virus becomes quickly resistant to new drugs. When the virus infects
a human cell it releases into the cell its capsid, a closed, stable
container protecting the viral genetic material. However, interaction
with the cell triggers at some point an instability of the capsid,
leading to a well timed release of the genetic material that merges
then with the cell's genes and begins to control the cell. The dual
role of the capsid, to be functionally both stable and unstable, makes
it in principle an ideal target for antiviral drugs and, in fact,
treatments of other viral infections successfully target the
respective capsids. The size of the HIV-1 capsid (about 1,300
proteins), and its irregular shape had prevented so far the resolution
of a full capsid atomic-level structure. However, in a tour de force
effort, groups of experimental and computational scientists have now
resolved the capsid's chemical structure (deposited to the protein
data bank under the accession codes 3J3Q
and 3J3Y).
As reported
recently (see also journal cover), the
researchers combined NMR structure analysis, electron microscopy and
data-guided molecular dynamics
simulations utilizing VMD to prepare
and analyze simulations performed using NAMD on one of the most powerful computers
worldwide, Blue
Waters, to obtain and characterize the HIV-1 capsid. The
discovery can guide now the design of novel drugs for enhanced
antiviral therapy.
More information is available on our virus website, in video, and in a press release.
|
|
See also movie: 15.5MB
made with VMD
|
|
Human immunodeficiency virus type 1 (HIV-1) is the major cause of
AIDS, for which treatments need to be developed continuously as the
virus becomes quickly resistant to new drugs. When the virus infects
a human cell it releases into the cell its capsid, a closed, stable
container protecting the viral genetic material. However, interaction
with the cell triggers at some point an instability of the capsid,
leading to a well timed release of the genetic material that merges
then with the cell's genes and begins to control the cell. The dual
role of the capsid, to be functionally both stable and unstable, makes
it in principle an ideal target for antiviral drugs and, in fact,
treatments of other viral infections successfully target the
respective capsids. The size of the HIV-1 capsid (about 1,300
proteins), and its irregular shape had prevented so far the resolution
of a full capsid atomic-level structure. However, in a tour de force
effort, groups of experimental and computational scientists have now
resolved the capsid's chemical structure (deposited to the protein
data bank under the accession codes 3J3Q
and 3J3Y).
As reported
recently (see also journal cover), the
researchers combined NMR structure analysis, electron microscopy and
data-guided molecular dynamics
simulations utilizing VMD to prepare
and analyze simulations performed using NAMD on one of the most powerful computers
worldwide, Blue
Waters, to obtain and characterize the HIV-1 capsid. The
discovery can guide now the design of novel drugs for enhanced
antiviral therapy.
More information is available on our virus website, in video, and in a press release.
|
|
See also movie: 15.5MB
made with VMD
|
|
Human immunodeficiency virus type 1 (HIV-1) is the major cause of
AIDS, for which treatments need to be developed continuously as the
virus becomes quickly resistant to new drugs. When the virus infects
a human cell it releases into the cell its capsid, a closed, stable
container protecting the viral genetic material. However, interaction
with the cell triggers at some point an instability of the capsid,
leading to a well timed release of the genetic material that merges
then with the cell's genes and begins to control the cell. The dual
role of the capsid, to be functionally both stable and unstable, makes
it in principle an ideal target for antiviral drugs and, in fact,
treatments of other viral infections successfully target the
respective capsids. The size of the HIV-1 capsid (about 1,300
proteins), and its irregular shape had prevented so far the resolution
of a full capsid atomic-level structure. However, in a tour de force
effort, groups of experimental and computational scientists have now
resolved the capsid's chemical structure (deposited to the protein
data bank under the accession codes 3J3Q
and 3J3Y).
As reported
recently (see also journal cover), the
researchers combined NMR structure analysis, electron microscopy and
data-guided molecular dynamics
simulations utilizing VMD to prepare
and analyze simulations performed using NAMD on one of the most powerful computers
worldwide, Blue
Waters, to obtain and characterize the HIV-1 capsid. The
discovery can guide now the design of novel drugs for enhanced
antiviral therapy.
More information is available on our virus website, in video, and in a press release.
|
|
See also movie: 15.5MB
made with VMD
|
|
Human immunodeficiency virus type 1 (HIV-1) is the major cause of
AIDS, for which treatments need to be developed continuously as the
virus becomes quickly resistant to new drugs. When the virus infects
a human cell it releases into the cell its capsid, a closed, stable
container protecting the viral genetic material. However, interaction
with the cell triggers at some point an instability of the capsid,
leading to a well timed release of the genetic material that merges
then with the cell's genes and begins to control the cell. The dual
role of the capsid, to be functionally both stable and unstable, makes
it in principle an ideal target for antiviral drugs and, in fact,
treatments of other viral infections successfully target the
respective capsids. The size of the HIV-1 capsid (about 1,300
proteins), and its irregular shape had prevented so far the resolution
of a full capsid atomic-level structure. However, in a tour de force
effort, groups of experimental and computational scientists have now
resolved the capsid's chemical structure (deposited to the protein
data bank under the accession codes 3J3Q
and 3J3Y).
As reported
recently (see also journal cover), the
researchers combined NMR structure analysis, electron microscopy and
data-guided molecular dynamics
simulations utilizing VMD to prepare
and analyze simulations performed using NAMD on one of the most powerful computers
worldwide, Blue
Waters, to obtain and characterize the HIV-1 capsid. The
discovery can guide now the design of novel drugs for enhanced
antiviral therapy.
More information is available on our virus website, in video, and in a press release.
|
|
See also movie: 15.5MB
made with VMD
|
|
Human immunodeficiency virus type 1 (HIV-1) is the major cause of
AIDS, for which treatments need to be developed continuously as the
virus becomes quickly resistant to new drugs. When the virus infects
a human cell it releases into the cell its capsid, a closed, stable
container protecting the viral genetic material. However, interaction
with the cell triggers at some point an instability of the capsid,
leading to a well timed release of the genetic material that merges
then with the cell's genes and begins to control the cell. The dual
role of the capsid, to be functionally both stable and unstable, makes
it in principle an ideal target for antiviral drugs and, in fact,
treatments of other viral infections successfully target the
respective capsids. The size of the HIV-1 capsid (about 1,300
proteins), and its irregular shape had prevented so far the resolution
of a full capsid atomic-level structure. However, in a tour de force
effort, groups of experimental and computational scientists have now
resolved the capsid's chemical structure (deposited to the protein
data bank under the accession codes 3J3Q
and 3J3Y).
As reported
recently (see also journal cover), the
researchers combined NMR structure analysis, electron microscopy and
data-guided molecular dynamics
simulations utilizing VMD to prepare
and analyze simulations performed using NAMD on one of the most powerful computers
worldwide, Blue
Waters, to obtain and characterize the HIV-1 capsid. The
discovery can guide now the design of novel drugs for enhanced
antiviral therapy.
More information is available on our virus website, in video, and in a press release.
|
|
See also movie: 15.5MB
made with VMD
|
|
Human immunodeficiency virus type 1 (HIV-1) is the major cause of
AIDS, for which treatments need to be developed continuously as the
virus becomes quickly resistant to new drugs. When the virus infects
a human cell it releases into the cell its capsid, a closed, stable
container protecting the viral genetic material. However, interaction
with the cell triggers at some point an instability of the capsid,
leading to a well timed release of the genetic material that merges
then with the cell's genes and begins to control the cell. The dual
role of the capsid, to be functionally both stable and unstable, makes
it in principle an ideal target for antiviral drugs and, in fact,
treatments of other viral infections successfully target the
respective capsids. The size of the HIV-1 capsid (about 1,300
proteins), and its irregular shape had prevented so far the resolution
of a full capsid atomic-level structure. However, in a tour de force
effort, groups of experimental and computational scientists have now
resolved the capsid's chemical structure (deposited to the protein
data bank under the accession codes 3J3Q
and 3J3Y).
As reported
recently (see also journal cover), the
researchers combined NMR structure analysis, electron microscopy and
data-guided molecular dynamics
simulations utilizing VMD to prepare
and analyze simulations performed using NAMD on one of the most powerful computers
worldwide, Blue
Waters, to obtain and characterize the HIV-1 capsid. The
discovery can guide now the design of novel drugs for enhanced
antiviral therapy.
More information is available on our virus website, in video, and in a press release.
|
|
See also movie: 15.5MB
made with VMD
|
|
Human immunodeficiency virus type 1 (HIV-1) is the major cause of
AIDS, for which treatments need to be developed continuously as the
virus becomes quickly resistant to new drugs. When the virus infects
a human cell it releases into the cell its capsid, a closed, stable
container protecting the viral genetic material. However, interaction
with the cell triggers at some point an instability of the capsid,
leading to a well timed release of the genetic material that merges
then with the cell's genes and begins to control the cell. The dual
role of the capsid, to be functionally both stable and unstable, makes
it in principle an ideal target for antiviral drugs and, in fact,
treatments of other viral infections successfully target the
respective capsids. The size of the HIV-1 capsid (about 1,300
proteins), and its irregular shape had prevented so far the resolution
of a full capsid atomic-level structure. However, in a tour de force
effort, groups of experimental and computational scientists have now
resolved the capsid's chemical structure (deposited to the protein
data bank under the accession codes 3J3Q
and 3J3Y).
As reported
recently (see also journal cover), the
researchers combined NMR structure analysis, electron microscopy and
data-guided molecular dynamics
simulations utilizing VMD to prepare
and analyze simulations performed using NAMD on one of the most powerful computers
worldwide, Blue
Waters, to obtain and characterize the HIV-1 capsid. The
discovery can guide now the design of novel drugs for enhanced
antiviral therapy.
More information is available on our virus website, in video, and in a press release.
|
|
See also movie: 15.5MB
made with VMD
|
|
Human immunodeficiency virus type 1 (HIV-1) is the major cause of
AIDS, for which treatments need to be developed continuously as the
virus becomes quickly resistant to new drugs. When the virus infects
a human cell it releases into the cell its capsid, a closed, stable
container protecting the viral genetic material. However, interaction
with the cell triggers at some point an instability of the capsid,
leading to a well timed release of the genetic material that merges
then with the cell's genes and begins to control the cell. The dual
role of the capsid, to be functionally both stable and unstable, makes
it in principle an ideal target for antiviral drugs and, in fact,
treatments of other viral infections successfully target the
respective capsids. The size of the HIV-1 capsid (about 1,300
proteins), and its irregular shape had prevented so far the resolution
of a full capsid atomic-level structure. However, in a tour de force
effort, groups of experimental and computational scientists have now
resolved the capsid's chemical structure (deposited to the protein
data bank under the accession codes 3J3Q
and 3J3Y).
As reported
recently (see also journal cover), the
researchers combined NMR structure analysis, electron microscopy and
data-guided molecular dynamics
simulations utilizing VMD to prepare
and analyze simulations performed using NAMD on one of the most powerful computers
worldwide, Blue
Waters, to obtain and characterize the HIV-1 capsid. The
discovery can guide now the design of novel drugs for enhanced
antiviral therapy.
More information is available on our virus website, in video, and in a press release.
|
|
See also movie: 15.5MB
made with VMD
|
|
Human immunodeficiency virus type 1 (HIV-1) is the major cause of
AIDS, for which treatments need to be developed continuously as the
virus becomes quickly resistant to new drugs. When the virus infects
a human cell it releases into the cell its capsid, a closed, stable
container protecting the viral genetic material. However, interaction
with the cell triggers at some point an instability of the capsid,
leading to a well timed release of the genetic material that merges
then with the cell's genes and begins to control the cell. The dual
role of the capsid, to be functionally both stable and unstable, makes
it in principle an ideal target for antiviral drugs and, in fact,
treatments of other viral infections successfully target the
respective capsids. The size of the HIV-1 capsid (about 1,300
proteins), and its irregular shape had prevented so far the resolution
of a full capsid atomic-level structure. However, in a tour de force
effort, groups of experimental and computational scientists have now
resolved the capsid's chemical structure (deposited to the protein
data bank under the accession codes 3J3Q
and 3J3Y).
As reported
recently (see also journal cover), the
researchers combined NMR structure analysis, electron microscopy and
data-guided molecular dynamics
simulations utilizing VMD to prepare
and analyze simulations performed using NAMD on one of the most powerful computers
worldwide, Blue
Waters, to obtain and characterize the HIV-1 capsid. The
discovery can guide now the design of novel drugs for enhanced
antiviral therapy.
More information is available on our virus website, in video, and in a press release.
|
|
See also movie: 15.5MB
made with VMD
|
|
Human immunodeficiency virus type 1 (HIV-1) is the major cause of
AIDS, for which treatments need to be developed continuously as the
virus becomes quickly resistant to new drugs. When the virus infects
a human cell it releases into the cell its capsid, a closed, stable
container protecting the viral genetic material. However, interaction
with the cell triggers at some point an instability of the capsid,
leading to a well timed release of the genetic material that merges
then with the cell's genes and begins to control the cell. The dual
role of the capsid, to be functionally both stable and unstable, makes
it in principle an ideal target for antiviral drugs and, in fact,
treatments of other viral infections successfully target the
respective capsids. The size of the HIV-1 capsid (about 1,300
proteins), and its irregular shape had prevented so far the resolution
of a full capsid atomic-level structure. However, in a tour de force
effort, groups of experimental and computational scientists have now
resolved the capsid's chemical structure (deposited to the protein
data bank under the accession codes 3J3Q
and 3J3Y).
As reported
recently (see also journal cover), the
researchers combined NMR structure analysis, electron microscopy and
data-guided molecular dynamics
simulations utilizing VMD to prepare
and analyze simulations performed using NAMD on one of the most powerful computers
worldwide, Blue
Waters, to obtain and characterize the HIV-1 capsid. The
discovery can guide now the design of novel drugs for enhanced
antiviral therapy.
More information is available on our virus website, in video, and in a press release.
|
|
See also movie: 15.5MB
made with VMD
|
|
Human immunodeficiency virus type 1 (HIV-1) is the major cause of
AIDS, for which treatments need to be developed continuously as the
virus becomes quickly resistant to new drugs. When the virus infects
a human cell it releases into the cell its capsid, a closed, stable
container protecting the viral genetic material. However, interaction
with the cell triggers at some point an instability of the capsid,
leading to a well timed release of the genetic material that merges
then with the cell's genes and begins to control the cell. The dual
role of the capsid, to be functionally both stable and unstable, makes
it in principle an ideal target for antiviral drugs and, in fact,
treatments of other viral infections successfully target the
respective capsids. The size of the HIV-1 capsid (about 1,300
proteins), and its irregular shape had prevented so far the resolution
of a full capsid atomic-level structure. However, in a tour de force
effort, groups of experimental and computational scientists have now
resolved the capsid's chemical structure (deposited to the protein
data bank under the accession codes 3J3Q
and 3J3Y).
As reported
recently (see also journal cover), the
researchers combined NMR structure analysis, electron microscopy and
data-guided molecular dynamics
simulations utilizing VMD to prepare
and analyze simulations performed using NAMD on one of the most powerful computers
worldwide, Blue
Waters, to obtain and characterize the HIV-1 capsid. The
discovery can guide now the design of novel drugs for enhanced
antiviral therapy.
More information is available on our virus website, in video, and in a press release.
|
|
See also movie: 15.5MB
made with VMD
|
|
Human immunodeficiency virus type 1 (HIV-1) is the major cause of
AIDS, for which treatments need to be developed continuously as the
virus becomes quickly resistant to new drugs. When the virus infects
a human cell it releases into the cell its capsid, a closed, stable
container protecting the viral genetic material. However, interaction
with the cell triggers at some point an instability of the capsid,
leading to a well timed release of the genetic material that merges
then with the cell's genes and begins to control the cell. The dual
role of the capsid, to be functionally both stable and unstable, makes
it in principle an ideal target for antiviral drugs and, in fact,
treatments of other viral infections successfully target the
respective capsids. The size of the HIV-1 capsid (about 1,300
proteins), and its irregular shape had prevented so far the resolution
of a full capsid atomic-level structure. However, in a tour de force
effort, groups of experimental and computational scientists have now
resolved the capsid's chemical structure (deposited to the protein
data bank under the accession codes 3J3Q
and 3J3Y).
As reported
recently (see also journal cover), the
researchers combined NMR structure analysis, electron microscopy and
data-guided molecular dynamics
simulations utilizing VMD to prepare
and analyze simulations performed using NAMD on one of the most powerful computers
worldwide, Blue
Waters, to obtain and characterize the HIV-1 capsid. The
discovery can guide now the design of novel drugs for enhanced
antiviral therapy.
More information is available on our virus website, in video, and in a press release.
|
|
See also movie: 15.5MB
made with VMD
|
|
Human immunodeficiency virus type 1 (HIV-1) is the major cause of
AIDS, for which treatments need to be developed continuously as the
virus becomes quickly resistant to new drugs. When the virus infects
a human cell it releases into the cell its capsid, a closed, stable
container protecting the viral genetic material. However, interaction
with the cell triggers at some point an instability of the capsid,
leading to a well timed release of the genetic material that merges
then with the cell's genes and begins to control the cell. The dual
role of the capsid, to be functionally both stable and unstable, makes
it in principle an ideal target for antiviral drugs and, in fact,
treatments of other viral infections successfully target the
respective capsids. The size of the HIV-1 capsid (about 1,300
proteins), and its irregular shape had prevented so far the resolution
of a full capsid atomic-level structure. However, in a tour de force
effort, groups of experimental and computational scientists have now
resolved the capsid's chemical structure (deposited to the protein
data bank under the accession codes 3J3Q
and 3J3Y).
As reported
recently (see also journal cover), the
researchers combined NMR structure analysis, electron microscopy and
data-guided molecular dynamics
simulations utilizing VMD to prepare
and analyze simulations performed using NAMD on one of the most powerful computers
worldwide, Blue
Waters, to obtain and characterize the HIV-1 capsid. The
discovery can guide now the design of novel drugs for enhanced
antiviral therapy.
More information is available on our virus website, in video, and in a press release.
|
|
See also movie: 15.5MB
made with VMD
|
|
Human immunodeficiency virus type 1 (HIV-1) is the major cause of
AIDS, for which treatments need to be developed continuously as the
virus becomes quickly resistant to new drugs. When the virus infects
a human cell it releases into the cell its capsid, a closed, stable
container protecting the viral genetic material. However, interaction
with the cell triggers at some point an instability of the capsid,
leading to a well timed release of the genetic material that merges
then with the cell's genes and begins to control the cell. The dual
role of the capsid, to be functionally both stable and unstable, makes
it in principle an ideal target for antiviral drugs and, in fact,
treatments of other viral infections successfully target the
respective capsids. The size of the HIV-1 capsid (about 1,300
proteins), and its irregular shape had prevented so far the resolution
of a full capsid atomic-level structure. However, in a tour de force
effort, groups of experimental and computational scientists have now
resolved the capsid's chemical structure (deposited to the protein
data bank under the accession codes 3J3Q
and 3J3Y).
As reported
recently (see also journal cover), the
researchers combined NMR structure analysis, electron microscopy and
data-guided molecular dynamics
simulations utilizing VMD to prepare
and analyze simulations performed using NAMD on one of the most powerful computers
worldwide, Blue
Waters, to obtain and characterize the HIV-1 capsid. The
discovery can guide now the design of novel drugs for enhanced
antiviral therapy.
More information is available on our virus website, in video, and in a press release.
|
|
See also movie: 15.5MB
made with VMD
|
|
Human immunodeficiency virus type 1 (HIV-1) is the major cause of
AIDS, for which treatments need to be developed continuously as the
virus becomes quickly resistant to new drugs. When the virus infects
a human cell it releases into the cell its capsid, a closed, stable
container protecting the viral genetic material. However, interaction
with the cell triggers at some point an instability of the capsid,
leading to a well timed release of the genetic material that merges
then with the cell's genes and begins to control the cell. The dual
role of the capsid, to be functionally both stable and unstable, makes
it in principle an ideal target for antiviral drugs and, in fact,
treatments of other viral infections successfully target the
respective capsids. The size of the HIV-1 capsid (about 1,300
proteins), and its irregular shape had prevented so far the resolution
of a full capsid atomic-level structure. However, in a tour de force
effort, groups of experimental and computational scientists have now
resolved the capsid's chemical structure (deposited to the protein
data bank under the accession codes 3J3Q
and 3J3Y).
As reported
recently (see also journal cover), the
researchers combined NMR structure analysis, electron microscopy and
data-guided molecular dynamics
simulations utilizing VMD to prepare
and analyze simulations performed using NAMD on one of the most powerful computers
worldwide, Blue
Waters, to obtain and characterize the HIV-1 capsid. The
discovery can guide now the design of novel drugs for enhanced
antiviral therapy.
More information is available on our virus website, in video, and in a press release.
|
|
See also movie: 15.5MB
made with VMD
|
|
Human immunodeficiency virus type 1 (HIV-1) is the major cause of
AIDS, for which treatments need to be developed continuously as the
virus becomes quickly resistant to new drugs. When the virus infects
a human cell it releases into the cell its capsid, a closed, stable
container protecting the viral genetic material. However, interaction
with the cell triggers at some point an instability of the capsid,
leading to a well timed release of the genetic material that merges
then with the cell's genes and begins to control the cell. The dual
role of the capsid, to be functionally both stable and unstable, makes
it in principle an ideal target for antiviral drugs and, in fact,
treatments of other viral infections successfully target the
respective capsids. The size of the HIV-1 capsid (about 1,300
proteins), and its irregular shape had prevented so far the resolution
of a full capsid atomic-level structure. However, in a tour de force
effort, groups of experimental and computational scientists have now
resolved the capsid's chemical structure (deposited to the protein
data bank under the accession codes 3J3Q
and 3J3Y).
As reported
recently (see also journal cover), the
researchers combined NMR structure analysis, electron microscopy and
data-guided molecular dynamics
simulations utilizing VMD to prepare
and analyze simulations performed using NAMD on one of the most powerful computers
worldwide, Blue
Waters, to obtain and characterize the HIV-1 capsid. The
discovery can guide now the design of novel drugs for enhanced
antiviral therapy.
More information is available on our virus website, in video, and in a press release.
|
|
See also movie: 15.5MB
made with VMD
|
|
Human immunodeficiency virus type 1 (HIV-1) is the major cause of
AIDS, for which treatments need to be developed continuously as the
virus becomes quickly resistant to new drugs. When the virus infects
a human cell it releases into the cell its capsid, a closed, stable
container protecting the viral genetic material. However, interaction
with the cell triggers at some point an instability of the capsid,
leading to a well timed release of the genetic material that merges
then with the cell's genes and begins to control the cell. The dual
role of the capsid, to be functionally both stable and unstable, makes
it in principle an ideal target for antiviral drugs and, in fact,
treatments of other viral infections successfully target the
respective capsids. The size of the HIV-1 capsid (about 1,300
proteins), and its irregular shape had prevented so far the resolution
of a full capsid atomic-level structure. However, in a tour de force
effort, groups of experimental and computational scientists have now
resolved the capsid's chemical structure (deposited to the protein
data bank under the accession codes 3J3Q
and 3J3Y).
As reported
recently (see also journal cover), the
researchers combined NMR structure analysis, electron microscopy and
data-guided molecular dynamics
simulations utilizing VMD to prepare
and analyze simulations performed using NAMD on one of the most powerful computers
worldwide, Blue
Waters, to obtain and characterize the HIV-1 capsid. The
discovery can guide now the design of novel drugs for enhanced
antiviral therapy.
More information is available on our virus website, in video, and in a press release.
|
|
See also movie: 15.5MB
made with VMD
|
|
Human immunodeficiency virus type 1 (HIV-1) is the major cause of
AIDS, for which treatments need to be developed continuously as the
virus becomes quickly resistant to new drugs. When the virus infects
a human cell it releases into the cell its capsid, a closed, stable
container protecting the viral genetic material. However, interaction
with the cell triggers at some point an instability of the capsid,
leading to a well timed release of the genetic material that merges
then with the cell's genes and begins to control the cell. The dual
role of the capsid, to be functionally both stable and unstable, makes
it in principle an ideal target for antiviral drugs and, in fact,
treatments of other viral infections successfully target the
respective capsids. The size of the HIV-1 capsid (about 1,300
proteins), and its irregular shape had prevented so far the resolution
of a full capsid atomic-level structure. However, in a tour de force
effort, groups of experimental and computational scientists have now
resolved the capsid's chemical structure (deposited to the protein
data bank under the accession codes 3J3Q
and 3J3Y).
As reported
recently (see also journal cover), the
researchers combined NMR structure analysis, electron microscopy and
data-guided molecular dynamics
simulations utilizing VMD to prepare
and analyze simulations performed using NAMD on one of the most powerful computers
worldwide, Blue
Waters, to obtain and characterize the HIV-1 capsid. The
discovery can guide now the design of novel drugs for enhanced
antiviral therapy.
More information is available on our virus website, in video, and in a press release.
|
|
See also movie: 15.5MB
made with VMD
|
|
Human immunodeficiency virus type 1 (HIV-1) is the major cause of
AIDS, for which treatments need to be developed continuously as the
virus becomes quickly resistant to new drugs. When the virus infects
a human cell it releases into the cell its capsid, a closed, stable
container protecting the viral genetic material. However, interaction
with the cell triggers at some point an instability of the capsid,
leading to a well timed release of the genetic material that merges
then with the cell's genes and begins to control the cell. The dual
role of the capsid, to be functionally both stable and unstable, makes
it in principle an ideal target for antiviral drugs and, in fact,
treatments of other viral infections successfully target the
respective capsids. The size of the HIV-1 capsid (about 1,300
proteins), and its irregular shape had prevented so far the resolution
of a full capsid atomic-level structure. However, in a tour de force
effort, groups of experimental and computational scientists have now
resolved the capsid's chemical structure (deposited to the protein
data bank under the accession codes 3J3Q
and 3J3Y).
As reported
recently (see also journal cover), the
researchers combined NMR structure analysis, electron microscopy and
data-guided molecular dynamics
simulations utilizing VMD to prepare
and analyze simulations performed using NAMD on one of the most powerful computers
worldwide, Blue
Waters, to obtain and characterize the HIV-1 capsid. The
discovery can guide now the design of novel drugs for enhanced
antiviral therapy.
More information is available on our virus website, in video, and in a press release.
|
|
See also movie: 15.5MB
made with VMD
|
|
Human immunodeficiency virus type 1 (HIV-1) is the major cause of
AIDS, for which treatments need to be developed continuously as the
virus becomes quickly resistant to new drugs. When the virus infects
a human cell it releases into the cell its capsid, a closed, stable
container protecting the viral genetic material. However, interaction
with the cell triggers at some point an instability of the capsid,
leading to a well timed release of the genetic material that merges
then with the cell's genes and begins to control the cell. The dual
role of the capsid, to be functionally both stable and unstable, makes
it in principle an ideal target for antiviral drugs and, in fact,
treatments of other viral infections successfully target the
respective capsids. The size of the HIV-1 capsid (about 1,300
proteins), and its irregular shape had prevented so far the resolution
of a full capsid atomic-level structure. However, in a tour de force
effort, groups of experimental and computational scientists have now
resolved the capsid's chemical structure (deposited to the protein
data bank under the accession codes 3J3Q
and 3J3Y).
As reported
recently (see also journal cover), the
researchers combined NMR structure analysis, electron microscopy and
data-guided molecular dynamics
simulations utilizing VMD to prepare
and analyze simulations performed using NAMD on one of the most powerful computers
worldwide, Blue
Waters, to obtain and characterize the HIV-1 capsid. The
discovery can guide now the design of novel drugs for enhanced
antiviral therapy.
More information is available on our virus website, in video, and in a press release.
|
|
See also movie: 15.5MB
made with VMD
|
|
Human immunodeficiency virus type 1 (HIV-1) is the major cause of
AIDS, for which treatments need to be developed continuously as the
virus becomes quickly resistant to new drugs. When the virus infects
a human cell it releases into the cell its capsid, a closed, stable
container protecting the viral genetic material. However, interaction
with the cell triggers at some point an instability of the capsid,
leading to a well timed release of the genetic material that merges
then with the cell's genes and begins to control the cell. The dual
role of the capsid, to be functionally both stable and unstable, makes
it in principle an ideal target for antiviral drugs and, in fact,
treatments of other viral infections successfully target the
respective capsids. The size of the HIV-1 capsid (about 1,300
proteins), and its irregular shape had prevented so far the resolution
of a full capsid atomic-level structure. However, in a tour de force
effort, groups of experimental and computational scientists have now
resolved the capsid's chemical structure (deposited to the protein
data bank under the accession codes 3J3Q
and 3J3Y).
As reported
recently (see also journal cover), the
researchers combined NMR structure analysis, electron microscopy and
data-guided molecular dynamics
simulations utilizing VMD to prepare
and analyze simulations performed using NAMD on one of the most powerful computers
worldwide, Blue
Waters, to obtain and characterize the HIV-1 capsid. The
discovery can guide now the design of novel drugs for enhanced
antiviral therapy.
More information is available on our virus website, in video, and in a press release.
|
|
See also movie: 15.5MB
made with VMD
|
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