- The 64-bit Mega is made available in two interfaces: graphical and command line. The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OS X. The command line Mega is available as native applications for Windows, Linux, and Mac OS X. They are intended for use in high-throughput and scripted.
- Moscito:- simulation software for molecular dynamics (MD) simulation.
Secret Worlds: The Universe Within - Soar through space starting at 10 million light years away from the Milky Way down through to a single proton in Florida in decreasing orders of magnitude (powers of ten). This tutorial explores the use of exponential notation to understand and compare the size of things in our world and the universe, and provides a glimpse of the duality between the macroworld around us and the hidden microworld within.
Alternative methods of using Molecular Workbench include: Running without Java Web Start » Using MW applets » Downloading an offline version » Something you should know about the Molecular Workbench software. MW runs on Windows, Mac OS X v10.4+, and Linux.
Electromagnetic Radiation Through dimensions (vbiog) mac os. - Visible light is a complex phenomenon that is classically explained with a simple model based on propagating rays and wavefronts, a concept first proposed in the late 1600s by Dutch physicist Christiaan Huygens. Electromagnetic radiation, the larger family of wave-like phenomena to which visible light belongs (also known as radiant energy), is the primary vehicle transporting energy through the vast reaches of the universe. The mechanisms by which visible light is emitted or absorbed by substances, and how it predictably reacts under varying conditions as it travels through space and the atmosphere, form the basis of the existence of color in our universe
Spinning Disk Confocal Microscopy - Spinning disk microscopy has advanced significantly in the past decade and now represents one of the optimum solutions for both routine and high-performance live-cell imaging applications. The rapid expansion in biomedical research using live-cell imaging techniques over the past several years has been fueled by a combination of events that include dramatic advances in spinning disk confocal microscopy instrumentation coupled with the introduction of novel ultra-sensitive detectors and continued improvements in the performance of genetically-encoded fluorescent proteins.
Spectral Imaging and Linear Unmixing - Spectral imaging and linear unmixing is becoming an important staple in the microscopist's toolbox, particularly when applied to the elimination of autofluorescence and for FRET investigations. Instruments equipped for spectral imaging are becoming increasingly popular and many confocal microscopes now offer this capability. Widefield fluorescence and brightfield microscopy are also being used more frequently for resolving complex fluorophore and absorbing dye mixtures, a trend that should continue into the future.
Fluorescent Protein Technology - It took over thirty years, and the advent of recombinant DNA as well as vastly improved molecular biological approaches to see the pioneering work of Osamu Shimomura developed into a useful tool for live-cell imaging by Doug Prasher and Martin Chalfie. Just in the past decade, however, we have witnessed a truly remarkable expansion in the fluorescent protein palette, largely driven by the innovative studies from Roger Tsien's laboratory. Most of the fluorescent proteins that are commonly used today have been modified through mutagenesis to optimize their expression in biological systems. Continued efforts using directed evolution approaches will no doubt improve the spectral characteristics, photostability, maturation time, brightness, acid resistance, and utility of the fluorescent protein tags for cellular imaging.
Carl Zeiss MicroImaging Online Campus - Visit the new ZEISS website that explores the fascinating world of optical microscopy and provides the necessary background to understand both the basic concepts and advanced principles. Included are review articles, interactive Flash tutorials, reference materials, and image galleries.
Light Sources for Optical Microscopy - The performance of the various illumination sources available for optical microscopy depends on the emission characteristics and geometry of the source, as well as the focal length, magnification and numerical aperture of the collector lens system. In gauging the suitability of a particular light source, the important parameters are structure (the spatial distribution of light, source geometry, coherence, and alignment), the wavelength distribution, spatial and temporal stability, brightness, and to what degree these various parameters can be controlled.
Mag Lab U: Learning about Electricity and Magnetism - Visit our sister website for interactive Java tutorials, a timeline of historical events, a museum of antique devices, and articles on topics related to electricity and magnetism.
Live-Cell Imaging - An increasing number of investigations are using live-cell imaging techniques to provide critical insight into the fundamental nature of cellular and tissue function, especially due to the rapid advances that are currently being witnessed in fluorescent protein and synthetic fluorophore technology. As such, live-cell imaging has become a requisite analytical tool in most cell biology laboratories, as well as a routine methodology that is practiced in the wide ranging fields of neurobiology, developmental biology, pharmacology, and many of the other related biomedical research disciplines. Among the most significant technical challenges for performing successful live-cell imaging experiments is to maintain the cells in a healthy state and functioning normally on the microscope stage while being illuminated in the presence of synthetic fluorophores and/or fluorescent proteins.
Comparing Confocal and Widefield Fluorescence Microscopy - Confocal microscopy offers several distinct advantages over traditional widefield fluorescence microscopy, including the ability to control depth of field, elimination or reduction of background information away from the focal plane (that leads to image degradation), and the capability to collect serial optical sections from thick specimens. The basic key to the confocal approach is the use of spatial filtering techniques to eliminate out-of-focus light or glare in specimens whose thickness exceeds the dimensions of the focal plane. This interactive tutorial explores and compares the differences between specimens when viewed in a confocal versus a widefield fluorescence microscope.
Fluorescence (Förster) Resonance Energy Transfer with Fluorescent Proteins - Fluorescent proteins are increasingly being applied as non-invasive probes in living cells due to their ability to be genetically fused to proteins of interest for investigations of localization, transport, and dynamics. In addition, the spectral properties of fluorescent proteins are ideal for measuring the potential for intracellular molecular interactions using the technique of Förster (or fluorescence) resonance energy transfer (FRET) microscopy. Because energy transfer is limited to distances of less than 10 nanometers, the detection of FRET provides valuable information about the spatial relationships of fusion proteins on a sub-resolution scale. This interactive tutorial explores various combinations of fluorescent proteins as potential FRET partners and provides information about critical resonance energy transfer parameters, as well as suggestions for microscope optical filter and light source configuration.
The Fluorescent Protein Color Palette - A broad range of fluorescent protein genetic variants have been developed over the past several years that feature fluorescence emission spectral profiles spanning almost the entire visible light spectrum. Extensive mutagenesis efforts in the original jellyfish protein have resulted in new fluorescent probes that range in color from blue to yellow and are some of the most widely used in vivo reporter molecules in biological research. Longer wavelength fluorescent proteins, emitting in the orange and red spectral regions, have been developed from the marine anemone Discosoma striata and reef corals belonging to the class Anthozoa. Still other species have been mined to produce similar proteins having cyan, green, yellow, orange, red, and far-red fluorescence emission. Developmental research efforts are ongoing to improve the brightness and stability of fluorescent proteins, thus improving their overall usefulness.
Introduction to Image Processing and Analysis - John Russ has taught hands-on courses and extended workshops in image processing and analysis to more than 3000 students, worldwide, over the course of his career. His one-day tutorials and lectures, sponsored by various professional societies and other organizations, have reached several thousand more. But the need to have a basic understanding of these topics is far wider than he can ever reach in person. Potentially everyone working with images, and certainly that includes every microscopist, needs to be aware of the possibilities (and limitations) of computer-based image processing and measurement. The descriptive reviews and interactive tutorials in this section cover most of the topics that the author discusses in typical one-day tutorials.
Fluorescent Protein Fluorophore Maturation Mechanisms - Autocatalytic formation of the fluorophore (also referred to as a chromophore) within the shielded environment of the polypeptide backbone during fluorescent protein maturation follows a surprisingly unified mechanism, especially considering the diverse natural origins of these useful biological probes. Shortly after synthesis, most fluorescent proteins slowly mature through a multi-step process that consists of folding, initial fluorophore ring cyclization, and subsequent modifications of the fluorophore. The spectral properties of fluorescent proteins are dependent upon the structure of the fluorophore as well as the localized interactions of amino acid residues in the immediate vicinity, and in some cases, residues far removed from the fluorophore. The interactive tutorials in this section explore fluorophore formation in a wide variety of spectrally diverse fluorescent proteins deduced from crystallographic studies.
The Virtual Rat - The humble rat has had an outsized impact on human history. In the Middle Ages, the black rat (Rattus rattus) was blamed for spreading the Black Plague through its fleas, a pandemic that killed a third of Europe's population, an estimated 34 million people. In modern times, however, a larger cousin, the Brown rat (Rattus norvegicus) has become an important model organism in biological research. Selective breeding of the Brown Rat has produced the albino laboratory rat. Rats grow quickly to sexual maturity and are easy to keep and breed in captivity. Scientists have bred many strains or 'lines' of rats specifically for experimentation. Generally, these lines are not transgenic because the easy techniques of genetic transformation that work in mice do not work as well for rats. This has been a problem for investigators who view rat behavior and physiology as more relevant to humans and easier to observe than in mice. In October 2003, researchers succeeded in cloning two laboratory rats by the problematic technique of nuclear transfer. As cloning techniques are perfected, rats likely will become an important subject of genetic research.
Rat Brain Tissue Sections - The rat brain has served as an excellent model for elucidating the complex anatomy and physiological mechanisms of the human brain. As a result, a significant amount of information on brain diseases, such as dementia and Parkinson's disease, has been determined from investigations using rat brains. Brain tissue has been mapped into dozens of major and hundreds of minor regions that are anatomically and functionally distinct. Individual brain cells segregate into specialized areas by expressing a wide spectrum of specific housekeeping proteins, enzymes, transporters, and receptors. This digital image gallery explores many regions of the rat brain as observed with immunofluorescence in coronal, horizontal, and sagittal thick sections using laser scanning confocal microscopy.
Cells in Motion - In multicellular tissues, such as those found in animals and humans, individual cells employ a variety of locomotion mechanisms to maneuver through spaces in the extracellular matrix and over the surfaces of other cells. Examples are the rapid movement of cells in developing embryos, organ-to-organ spreading of malignant cancer cells, and the migration of neural axons to synaptic targets. Unlike single-celled swimming organisms, crawling cells in culture do not possess cilia or flagella, but tend to move by coordinated projection of the cytoplasm in repeating cycles of extension and retraction that deform the entire cell. The digital videos presented in this gallery investigate animal cell motility patterns in a wide variety of morphologically different specimens. Requires the RealPlayer browser plug-in.
Laser Scanning Confocal Microscope Simulator - Perhaps the most significant advance in optical microscopy during the past decade has been the refinement of mainstream laser scanning confocal microscope (LSCM) techniques using improved synthetic fluorescent probes and genetically engineered proteins, a wider spectrum of laser light sources coupled to highly accurate acousto-optic tunable filter control, and the combination of more advanced software packages with modern high-performance computers. This interactive tutorial explores multi-laser fluorescence and differential interference contrast (DIC) confocal imaging using the Olympus FluoView FV1000 confocal microscope software interface as a model.
Nikon MicroscopyU - The MicroscopyU website is designed to provide an educational forum for all aspects of optical microscopy, digital imaging, and photomicrography. Together with the scientists and programmers at Molecular Expressions, Nikon microscopists and engineers are providing the latest state-of-the-art information in microscope optics and imaging technology including specialized techniques such as fluorescence, differential interference contrast (DIC), phase contrast, reflected light microscopy, and microscopy of living cells. We invite you to explore MicroscopyU and discover more about the exciting world of optics and microscopy.
Olympus Image of the Year Award - Inspired by the beauty and breadth of images submitted for the 2018 Image of the Year Award held in Europe, Olympus is continuing to search for the best light microscopy images in 2019—this time on a global scale. Olympus' first Image of the Year Global Life Science Light Microscopy Award recognizes the very best in life science imaging worldwide.
Fluorescence Microscopy of Cells in Culture - Serious attempts at the culture of whole tissues and isolated cells were first undertaken in the early 1900s as a technique for investigating the behavior of animal cells in an isolated and highly controlled environment. The term tissue culture arose because most of the early cells were derived from primary tissue explants, a technique that dominated the field for over 50 years. As established cell lines emerged, the application of well-defined normal and transformed cells in biomedical investigations has become an important staple in the development of cellular and molecular biology. This fluorescence image gallery explores over 30 of the most common cell lines, labeled with a variety of fluorophores using both traditional staining methods as well as immunofluorescence techniques.
Human Pathology Digital Image Gallery - The investigation of disease in humans has, understandably, been one of the primary focal points in medicine for thousands of years. The image gallery presented in this section attempts to illustrate, through use of the brightfield microscope, many of the pathological conditions that are readily observed in stained human specimens. Each image was chosen for artistic merit, photographic quality, and content. Note that several of the images in this gallery might not depict every aspect of the pathological condition under which they are catalogued.
Nikon Fluorescence Microscopy Digital Image Gallery - The widefield reflected light fluorescence microscope has been a fundamental tool for the examination of fluorescently labeled cells and tissues since the introduction of the dichromatic mirror in the late 1940s. Furthermore, advances in synthetic fluorophore design coupled to the vast array of commercially available primary and secondary antibodies have provided the biologist with a powerful arsenal in which to probe the minute structural details of living organisms with this technique. In the late twentieth century, the discovery and directed mutagenesis of fluorescent proteins added to the cadre of tools and created an avenue for scientists to probe the dynamics of living cells in culture. This gallery examines the fluorescence microscopy of both cells and tissues with a wide spectrum of fluorescent probes.
Burgers 'n Fries - Join us for a microscopic examination of America's culinary favorite: the ubiquitous hamburger and French fries. Discover how this delightful classic is just as beautiful as it is tasty.
Chemical Crystals - Chemical compounds can exist in three basic phases, gaseous, liquid, or solid. Gases consist of weakly bonded atoms and expand to fill any available space. Solids are characterized by strong atomic bonding and have a rigid shape. Most are crystalline, having a three-dimensional periodic atomic arrangement. Some, such as glass, lack this periodic arrangement and are noncrystalline, or amorphous. Liquids have characteristics that fall in between gases and solids. This cinemicrographic collection presents time-lapse movies of various chemical compounds as they change physical states.
Scanning Electron Microscopy - We have teamed up with award-winning electron microscopist Dennis Kunkel to produce a virtual Scanning Electron Microscope (vSEM). Visitors can adjust the focus, contrast, and magnification of microscopic creatures viewed at thousands of times their actual size.
Laser Scanning Confocal Microscopy - (approximately a 30 second download on 28.8K modems) Several methods have been developed to overcome the poor contrast inherent with imaging thick specimens in a conventional microscope. Specimens having a moderate degree of thickness (5 to 15 microns) will produce dramatically improved images with either confocal or deconvolution techniques. The thickest specimens (20 microns and above) will suffer from a tremendous amount of extraneous light in out-of-focus regions, and are probably best-imaged using confocal techniques. This tutorial explores imaging specimens through serial z-axis optical sections utilizing a virtual confocal microscope.
Stereoscopic Zoom Microscopy - Many stereoscopic microscopes feature the ability to perform a continuous magnification change by means of a zoom lens system placed between the objective and the eyepieces. Explore zoom magnification, focus, and illumination intensity in stereoscopic microscopes with this interactive Flash tutorial.
Java-powered QX3 Computer Web Microscope - This virtual QX3 microscope is broadcasting images over the Web at 20 frames/second, which can be viewed in a specially designed Java client run through your Web browser at frame rates up to 18 frames/second. No additional software is needed, but don't try this unless you have a fast connection (10 Mbits/sec Ethernet or higher). With this software, you can capture single digital images, record movies, and perform time-lapse cinematography experiments.
Museum of Microscopy - Featuring 3-D Studio Max drawings of ancient microscopes, this unique gallery explores many of the historic microscopes made during the last four centuries. Visit the gallery and download a copy of our Windows screen saver containing selected images of these beautiful microscopes.
Silicon Zoo - This popular gallery features images of cartoon characters and other doodling placed onto computer chips by their designers. Ratlab mac os.
Featured Microscopist - Our featured microscopist for Spring 2002 is noted Dutch photomicrographer Loes Modderman. Born in Amsterdam in 1944, Modderman received her first microscope by age 13 and has never lost her sense of wonder at the minute beauties available with this instrument. Many years ago, Loes initiated a series of chemical crystallization experiments, which allowed her to meld longtime interests in nature, art, science, and photography to form her abstract photomicrographs into a colorful celebration of form and structure. A wide spectrum of these photomicrographs are featured in this gallery.
Cell and Virus Structure - Although the human body contains over 75 trillion cells, the majority of life forms exist as single cells that perform all the functions necessary for independent existence. Most cells are far too small to be seen with the naked eye and require the use of high-power optical and electron microscopes for careful examination. Space blood - s02e06 mac os.
Fluorescence Microscopy Digital Image Gallery - Featuring specimens collected from a wide spectrum of disciplines, the fluorescence gallery contains a variety of examples using both specific fluorochrome stains and autofluorescence. Images were captured utilizing either a Nikon DXM 1200 digital camera, an Optronics MagnaFire Peltier-cooled camera, or classical photomicrography on film with Fujichrome Provia 35 millimeter transparency film.
Molecular Mac Os Catalina
Pond Life - Freshwater ponds provide a home for a wide variety of aquatic and semi-aquatic plants, insects, and animals. The vast majority of pond inhabitants, however, are invisible until viewed under the microscope. Beneath the placid surface of any pond is a microscopic metropolis bustling with activity as tiny bizarre organisms pursue their lives; locomoting, eating, trying not to be eaten, excreting, and reproducing. In this collection of digital movies, observe the activities of microscopic organisms taken from a typical North Florida pond.
Concepts in Digital Imaging Technology - Explore the basic concepts in digital imaging with our illustrated discussions and interactive tutorials. Topics covered include CCD operation, image capture, digital manipulation of images and a wide spectrum of other issues in this emerging field.
Science, Optics & You - Explore our science curriculum package being developed for teachers, students, and parents. Activities are designed to promote the asking and answering of questions related to light, color, and optics. The program begins with basic information about lenses, shadows, prisms, and color, leading up to the use of sophisticated instruments scientists use to help them understand the world.
Intel Play QX3 Computer Microscope - Take a moment to visit our in-depth discussion of this incredible toy microscope. Included topics are the QX3 hardware (microscope), interactive microscope software, suggested specialized techniques, and digital image galleries from the QX3 microscope.
Creative Photomicrography - By employing multiple exposure photomicrography, we have succeeded in generating a series of unusual micrographs which we have termed microscapes. These micrographs are intended to resemble surrealistic/alien landscapes.
Welcome! | Garrett M. Morris David S. Goodsell Ruth Huey William Lindstrom William E. Hart Scott Kurowski Scott Halliday Rik Belew Arthur J. Olson |
What is AutoDock?
AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
Current distributions of AutoDock consist of two generations of software: AutoDock 4 and AutoDock Vina.
AutoDock 4 actually consists of two main programs: autodock performs the docking of the ligand to a set of grids describing the target protein; autogrid pre-calculates these grids.
In addition to using them for docking, the atomic affinity grids can be visualised. This can help, for example, to guide organic synthetic chemists design better binders.
AutoDock Vina does not require choosing atom types and pre-calculating grid maps for them. Instead, it calculates the grids internally, for the atom types that are needed, and it does this virtually instantly.
We have also developed a graphical user interface called AutoDockTools, or ADT for short, which amongst other things helps to set up which bonds will treated as rotatable in the ligand and to analyze dockings.
AutoDock has applications in:
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AutoDock 4 is free and is available under the GNU General Public License. AutoDock Vina is available under the Apache license, allowing commercial and non-commercial use and redistribution. Click on the 'Downloads' tab. And Happy Docking!
What is AutoDock Vina?
AutoDock Vina is a new generation of docking software from the Molecular Graphics Lab. It achieves significant improvements in the average accuracy of the binding mode predictions, while also being up to two orders of magnitude faster than AutoDock 4.1Because the scoring functions used by AutoDock 4 and AutoDock Vina are different and inexact, on any given problem, either program may provide a better result.
What's new?
June 1, 2009AutoDock 4.2 is faster than earlier versions, and it allows sidechains in the macromolecule to be flexible. As before, rigid docking is blindingly fast, and high-quality flexible docking can be done in around a minute. Up to 40,000 rigid dockings can be done in a day on one cpu.
AutoDock 4.2 now has a free-energy scoring function that is based on a linear regression analysis, the AMBER force field, and an even larger set of diverse protein-ligand complexes with known inhibition constants than we used in AutoDock 3.0. The best model was cross-validated with a separate set of HIV-1 protease complexes, and confirmed that the standard error is around 2.5 kcal/mol. This is enough to discriminate between leads with milli-, micro- and nano-molar inhibition constants.
You can read more about the new features in AutoDock 4.2 and how to use them in the AutoDock4.2 User Guide.
AutoDock 4 is Free Software
May 7, 2007The introduction of AutoDock 4 comprises three major improvements:
- The docking results are more accurate and reliable.
- It can optionally model flexibility in the target macromolecule.
- It enables AutoDock's use in evaluating protein-protein interactions.
AutoDock 4.0 not only is it faster than earlier versions, it allows sidechains in the macromolecule to be flexible. As before, rigid docking is blindingly fast, and high-quality flexible docking can be done in around a minute. Up to 40,000 rigid dockings can be done in a day on one cpu.
AutoDock 4.0 now has a free-energy scoring function that is based on a linear regression analysis, the AMBER force field, and an even larger set of diverse protein-ligand complexes with known inhibiton constants than we used in AutoDock 3.0. The best model was cross-validated with a separate set of HIV-1 protease complexes, and confirmed that the standard error is around 2.5 kcal/mol. This is enough to discriminate between leads with milli-, micro- and nano-molar inhibition constants.
You can read more details about the new features in AutoDock4.2 User Guide.
AutoDock 4.0 can be compiled to take advantiage of new search methods from the optimization library, ACRO, developed by William E. Hart at Sandia National Labs. We have also added some new features to our existing evolutionary methods. We still provide the Monte Carlo simulated annealing (SA) method of 2.4 and earlier. The Lamarckian Genetic Algorithm (LGA) is a big improvement on the Genetic Algorithm, and both genetic methods are much more efficient and robust than SA.
Mailing List and Forum
We have established a mailing list and forum for AutoDock users. Here is more information about the AutoDock List (ADL). URL for the forum is http://mgl.scripps.edu/forum.
What is AutoDockTools (ADT)?
We have developed and continue to improve our graphical front-end for AutoDock and AutoGrid, ADT (AutoDockTools). It runs on Linux, Mac OS X, SGI IRIX and Microsoft Windows. We also have new tutorials, along with accompanying sample files.
Where is AutoDock Used?
AutoDock has now been distributed to more than 29000 users around the world. It is being used in academic, governmental, non-profit and commercial settings. In January of 2011, a search of the ISI Citation Index showed more than 2700 publications have cited the primary AutoDock methods papers.
AutoDock is now distributed under the GPL open source license and is freely available for all to use. Because of the restrictions of incorporating GPL licensed software into other codes for the purpose of redistribution, some companies may wish to license AutoDock under a separate license agreement - which we can arrange. Please contact Prof. Arthur J. Olson at + 1 (858) 784-2526 for more information.
Why Use AutoDock?
AutoDock has been widely-used and there are many examples of its successful application in the literature (see References); in 2006, AutoDock was the most cited docking software. It is very fast, provides high quality predictions of ligand conformations, and good correlations between predicted inhibition constants and experimental ones. AutoDock has also been shown to be useful in blind docking, where the location of the binding site is not known. Plus, AutoDock is free software and version 4 is distributed under the GNU General Public License; it easy to obtain, too.
Run Your AutoDock Research Project on World Community Grid!
Molecular Mass Of Coh2
Does your research run on AutoDock? If so, you may be eligible to benefit from World Community Grid's free computational power to accelerate your research. AutoDock has already been 'grid-enabled' by World Community Grid's technical team and is run on World Community Grid with the following projects:
Mac Os Versions
- FightAIDS@Home project from The Scripps Research Institute.
- Discover Dengue Drugs - Together project from The University of Texas Medical Branch.
- Help Fight Childhood Cancer
Molecular Mass Of Koh
Please review World Community Grid's research project criteria and contact World Community Grid if you have an idea for a project proposal or any questions.
