Products

YASARA View is available for free and contains all the functions you need to explore a macromolecular structure interactively. As a bonus, you get YASARA's innovative 3D engine, which is up to 10 times faster than what you usually know from OpenGL, you can load multiple structures at the same time, create publication-quality ray-traced images including labels, and program your own macros and Python plugins. Included is YASARA Movie, a player for multimedia presentations and tutorials created with any of the higher stages, as well as the YASARA Python module to simply 'import yasara' in your Python scripts.

Key features:

• Cross-platform and easy installation: Windows, Linux and Mac OS X in the same directory, run directly from USB stick.
• Photo-realistic molecular graphics with full-scene antialiasing at resolutions up to 4K (3840×2160 pixels): up to 10 times faster than other OpenGL based solutions, even the ribosome rotates smoothly in CPK mode.
• Support for the latest GPU shader features like hardware tessellation, where the GPU increases the geometric details of polygon meshes (e.g. surfaces and secondary structure).
  
• Parallel (orthographic) and perspective projection.
• Interactive box, freehand/lasso or sphere selection tools.
  
• Support for over 70 molecular fileformats (based on OpenBabel).
• Download PDB files from the RCSB or the re-refined and improved version from  PDB_REDO.
  
• Optimal depth perception thanks to real-time shadows and ambient lighting, even on older hardware.
  
• All common graphics styles: CPK, balls & sticks, sticks, traces, tubes, ribbons, cartoons, labels, arrows.
• Interactive secondary structure morpher, which seamlessly interpolates between a realistic (close to Calpha) and an idealistic (perfectly straight strands and helices) secondary structure display, which can additionally be configured in countless ways to match your favorite secondary structure styling.
  
• Create alternative views of the scene, and switch between them using tabs at the top.
• Ray-tracing for publication quality graphics at arbitrary resolutions, interactively move the lightsource, adjust shadows.
• Color any PDB file by sequence conservation and quality indicators (automatically mapped from HSSP/PDBFinder2).
  
• Superpose structures and structure ensembles, calculate proper RMSDs (minimized by flipping equivalent atoms).
  
• Align multiple proteins based on their structure or sequence, using a variety of methods. Identify related structures in the PDB.
  
• Measure distances, angles, dihedrals.
• Build atoms, residues, peptide chains and mutate amino acids.
• Visualize contacts, hydrogen bonds, and hydrophobic/pi-pi/cation-pi interactions.
• Create realistic 3D structures from nonsense, 1D or 2D molecules, and convert them back to 2D structural formulas.
  
• Automatic assignment of fractional bond orders and missing hydrogen atoms, graph-theory based typing of hetero-polycycles.
• Analyze and change atomic B-factors and occupancies, rename and renumber atoms and residues.
• Extremely fast algorithms to show and update Van der Waals, molecular and solvent accessible surfaces in real-time.
  
• Extend YASARA with your own functions using the Python scripting language.
• Use YASARA from your Python scripts, simply 'import yasara'.
• Simple Yanaconda macro language to automate your work and create flexible animations.
• eLearning functions: interactive tutorials provide the knowledge about molecular structure, modeling and simulations

YASARA Model contains YASARA View and adds all the functions you need to explore, analyze and model small to macromolecules in a production environment. This includes many features you often miss: unlimited undo/redo, macro recorder, quad-buffered stereo with shutter glasses or stereoscopic screens. You can load thousands of structures at the same time, move them around independently and create multimedia presentations (YASARA Movies). These movies can be encoded as MPEGs and pasted into Powerpoint or played back with all stages of YASARA, including the free YASARA View.

Key features:

• All the features of YASARA View listed above are included, no need to keep a separate YASARA View installation.
  
• Fully immersive OpenGL 3D stereo graphics with sterescopic screens or shutter glasses. High quality GPU accelerated anaglyph stereo mode for red/cyan glasses, that tricks the brain into seeing full color and enables stereo also on notebooks. Red/cyan glasses are included. Ultra-high resolutions up to 8K (7680×4320 pixels).
  
• Create the fanciest molecular animations with automatic rotations, movements, zooms, text in 3D letters, texture mapping of PNG/JPG images and conversion to 3D objects.
  
• Encode animations in MPEG format, paste them into Powerpoint presentations. Export Alias Wavefront objects for use by 3DStudioMax and others.
  
• Import OpenOffice Impress and Microsoft Powerpoint presentations, add molecular animations to the slides.
  
• Work with thousands of structures at the same time, move them around independently.
• Extensive coordinate manipulation: center, join, transform, oligomerize, transfer fragments (e.g. loops) or replicate them (e.g. domains).
  
• Analyze contacts, hydrogen bonds, hydrophobic/pi-pi/cation-pi interactions and protein secondary structure.
• Align small molecules like ligands automatically, by superposing them on the largest common fragment.
  
• Measure distances, angles and dihedrals between groups of atoms like helices or planar side-chains.
• Change distances, angles and dihedrals interactively.
• Choose a default pH from 0 to 14 when assigning fractional bond orders and adding hydrogens.
• Interactively build small molecules in just seconds with a sophisticated builder that offers over 50 functional groups to choose from.
  
• Show and calculate Van der Waals, molecular and solvent accessible surfaces, distinguish between outer and inner surfaces, calculate volumes. Analyze and show cavities formed by these surfaces.
  
• Create multiple interactive cut-planes to look inside surfaces and other objects.
• Identify cis-peptide bonds and wrong stereoisomeres.
• Store the results of your analysis in tables, import them in Excel.
• Record macros or write them with a text editor.
• Batch-processing of large data sets directly from the GUI (graphical user interface).
• Support for special input devices like SpaceBall.
• Unlimited undo/redo.

YASARA Model costs 110 € / 126 $ for academic and 550 € / 632 $ for commercial use, including one year of support and updates. This price includes Windows, Linux and Android, Mac OS X costs 20% extra, red/cyan stereo glasses and shipping are included, customers in Austria have to add 20% VAT. Click here to order or get a quotation, or check the screenshots, the complete feature list, or the license details.

YASARA Dynamics contains YASARA Model and adds support for molecular simulations. In addition to YASARA's own force fields (NOVA, YAMBER) you can use other well known MD force fields like AMBER, and run accurate all-atom MD simulations in aqueous solution with Particle Mesh Ewald longrange electrostatics. YASARA Dynamics is not a "black box" with input and output files, but shows the MD simulation in real-time on screen. You can fully interact with the scene, pull atoms or whole molecules around and finally do the type of molecular modeling that Cyrus Levinthal already pioneered back in 1966 ("..do the same type of pulling and pushing in the computer that we can do with our hands while building actual models. ", cited from an article in Scientific American).

Key features:

• All features listed for YASARA View and YASARA Model above are included, no additional purchase needed.
  
• Prepare a simulation: clean proteins, predict pKas, assign protonation states, fill the simulation cell with water.
• Fastest molecular dynamics algorithms for CPU and GPU (see benchmarks, and note that MacOSX does not have reliable GPU support) and energy minimizations in non-periodic or periodic cells with cuboid or triclinic shape (including rhombic dodecahedrons for maximum performance).
  
• AMBER and newly developed force fields (NOVA, YAMBER) included, define your own force fields.
• Accurate treatment of long-range electrostatic interactions with the Particle Mesh Ewald approach.
• Parallel and reproducible simulations on multiple CPUs and CPU cores with close to ideal speedups.
  
• Constrain bond lengths and water molecules with LINCS and SETTLE to reach large timesteps.
• Calculate energies, binding energies and solvation energies using Poisson-Boltzmann or PME methods.
• Manipulate a simulation interactively: pull atoms or entire molecules around, fix and free atoms, add restraints, toggle force field terms.
• Calculate the electrostatic potential using Poisson-Boltzmann or PME methods, visualize the results as densities, contours or surfaces.
• Run simulations at the touch of a button even in the presence of ligands, thanks to fully automatic force field parameter assignment for the General Amber Force Field (GAFF). Semi-empirical QM point charges are calculated using either AM1BCC or AutoSMILES, a newly developed approach for hi-speed assignment of RESP library charges.
• Run simulations of membrane proteins at the touch of a button.
  
• Automatic correction of cis-peptide bonds or wrong stereoisomeres for homology model refinement.
• Geometry optimization and analysis with semi-empirical MNDO/AM1/PM3 quantum chemistry using YAPAC, a built-in customized derivative of MOPAC.
• Analyze trajectories for conformational changes, calculate time averages, RMSDs, RMSFs, RDFs and dynamic cross-correlation matrices.
  
• Read and write trajectories in Sim, MDCrd or XTC format.
• Build oligosaccharides interactively, with stepwise energy minimization.

YASARA Dynamics costs 275 € / 316 $ for academic and 2200 € / 2530 $ for commercial use, including one year of support and updates. This price includes Windows, Linux and Android, Mac OS X costs 20% extra, red/cyan stereo glasses and shipping are included, customers in Austria have to add 20% VAT. Click here to order or get a quotation, or check the screenshots, the complete feature list, the hardware recommendations for MD, or the license details.

YASARA Structure contains YASARA Dynamics and adds all the functions needed to predict and validate macromolecular structures, including ligand docking and highly accurate force fields with knowledge-based potentials. If you already own one of the other YASARA stages, you can upgrade easily, just contact us for a quote.

Key features:

• All features listed for YASARA View, YASARA Model and YASARA Dynamics above are included, no additional purchase needed.
  
• Small-molecule docking at the touch of a button, using tuned versions of AutoDock and VINA with automatic setup, receptor flexibility and multi-CPU support. Additional support for Fleksy, an induced fit docking program based on FlexX, developed at Organon/Schering-Plough.
• Side-chain rotamer prediction combining graph-theory and dead-end elimination with accurate treatment of electrostatics, solvation and subtle packing effects.
  
• Knowledge-based loop modeler with a compressed index of the PDB, peptide segments spanning selected anchor residues can be located within a fraction of a second, while considering sequence and secondary structure preferences. Loops can be optimized together with surrounding side-chains, considering all energy components including solvation.
  
• New force fields (YASARA and YASARA2) with multi-dimensional knowledge-based components for highly accurate refinement simulations to aid protein structure determination and prediction.
• Homology modeling at the touch of a button: select the target sequence and get a homology model, combined from multiple templates, refined in explicit solvent, as well as a detailed scientific report describing how the model was built, including extensive validation with figures and quality plots. Check the CASP results.
  
• pH dependent hydrogen bonding network optimizer, that automatically considers ligands and determines ambiguities in X-ray density.
• Built-in BLAST and PSI-BLAST, with automatically updated SwissProt, UniRef90, PDB and PDBC sequence databases, the latter augmented with WHAT_CHECK/ PDBFinder2 validation data to rank PDB structures sharing the same sequence.
• Secondary structure prediction with PsiPred and DSC.
  
• Extensive structure validation to judge the quality of experimental structures and models, based on a new combination of force field energies and Z-scores, that yields results not only for proteins, but for all organic molecules. This allows to validate for example protein-ligands interactions, an important aspect in drug design.
• Perform twisted structural alignments, where the protein is bent and wound to maximize the number of structurally aligned residues, for example to create sequence profiles for homology modeling
• Prediction and visualization of ion binding sites using valence scanning.
  

YASARA Structure costs 375 € / 431 $ for academic and 3300 € / 3795 $ for commercial use, including one year of support and updates. This price includes Windows and Linux, Mac OS X costs 20% extra, red/cyan stereo glasses and shipping are included, customers in Austria have to add 20% VAT. Click here to order or get a quotation, or check the screenshots,  the complete feature list, the hardware recommendations for MD, or the license details.

The YASARA NMR Module solves protein structures at the touch of a button, based on the protein sequence and distance-, dihedral-angle and RDC restraints. Input files are compatible with X-PLOR, folding and refinement are visualized in real-time on screen, allowing to identify problematic restraints. Floating assignments and non-standard residues are supported, all the details are described here.

The YASARA NMR Module is an add-on for YASARA Structure and costs 50 € / 57 $ for academic and 500 € / 575 $ for commercial use, including one year of support and updates. This price includes Windows and Linux, Mac OS X costs 20% extra, customers in Austria have to add 20% VAT. If you do not have YASARA Structure yet, click here to order or get a quotation and click here for license details, otherwise contact us directly.

The Bio-Prodict 3DM information systems are protein super-family platforms that collect, combine and integrate many different types of protein-related data. 3DM systems are designed to facilitate the exploration of sequence-structure-function relations, and have successfully been used many times to elucidate the function of individual amino acids, predict the effects of mutations, among others.

The 3DM platform is developed and distributed by Bio-Prodict, a CMBI spin-off company like YASARA Biosciences. Please contact for details and pricing information. An introductory movie can be watched at the Bio-Prodict site, more details about YASARA integration are available here.

The Twinset is a customized joint-distribution of WHAT IF and YASARA Dynamics or YASARA Structure (currently Linux and Windows only). With over 3500 citations, WHAT IF is a widely used program for structure validation and modeling. In the Twinset, WHAT IF inherits YASARA's user interface, graphics engine, macro language, unlimited undo/redo etc, so that WHAT IF functions become easily accessible.

The Twinset is freely available, but you need licenses for YASARA Dynamics or YASARA Structure and also WHAT IF. Click here for WHAT IF license details, and note that WHAT IF is now shareware/donationware. Customers in Austria have to add 20% VAT.

To order the Twinset, just place a normal order for YASARA Dynamics or YASARA Structure and then request the Twinset upgrade from . If you already own YASARA, email us your YASARA serial number.

Since April 2013, YASARA is available for selected Android smartphones and tablets, providing today's most feature-complete mobile molecular modeling environment, including interactive MD simulations. Tablet prices start at 175 EUR, two videos and all the details are available here.

Stereoscopic 3D molecular modeling hardware has become easily affordable, so that entire classrooms can enjoy this unique experience. The image on the right shows the easiest and cheapest solution: 3D vision is provided using 'passive stereo', where the images for left and right eye are shown in odd and even pixel lines and separated using flicker-free polarized glasses. The first popular screens with this feature were the Zalman ZM-M215W, ZM-M220W and ZM-M240W, costing around 200 EUR. Unfortunately it appears that Zalman discontinued this product line, so they are now mostly available as refurbished second hand models. But there are many follow up products, googling for passive stereo odd even finds e.g. the LG D2342P, the HP 2311x, the AOC e2352Phz or the Viewsonic V3D231. The big advantage is that this type of display is directly supported by YASARA with any graphics card and any operating system (no expensive Quadro/FireGL cards or special video drivers are needed). You can move your molecules through 3D space using the Connexion 3D SpaceNavigator with six degrees of freedom. Order now for 50 EUR.
Notes: The ZM-M220W has a resolution of 1680×1050 pixels. The polarized glasses ensure that the left eye sees only the odd pixel lines, while the right eye sees the even lines. So the resolution is reduced to 1680×525 pixels per eye as soon as the glasses are put on. This is hardly noticeable when looking at molecules, but becomes apparent when looking at characters. Text is therefore harder to read than with alternative, more expensive stereo solutions. Without glasses, the screen behaves just like any other screen and can be used for everyday work. It has a quite glossy surface, reflections can be a problem in bright rooms, but are hardly noticeable in somewhat darker 'molecular modeling caves'. At least YASARA Model is required.

If you want to demonstrate 3D modeling on a large screen, we recommend passive 3DTVs like the LG 42LB620V shown on the right. With a diagonal of 42" (107 cm), two polarized 3D glasses and a price of 380 EUR, this 3DTV is an excellent deal that will please your audience. Passive 3DTVs use exactly the same principle as described above for passive 3D computer screens, so they will work with any operating system and any graphics card, with YASARA running in window or fullscreen mode.
Notes: Make sure to buy a screen with a resolution of 1920×1080 pixels (FullHD). Since the images for left and right eye are shown in odd and even pixel lines, this leaves an effective resolution of 1920×540 pixels per eye, and you certainly do not want a lower resolution on such a large screen. Higher resolutions would of course be even better, but will only be supported by YASARA later this year and also require an advanced GPU with HDMI 2.0 connection. It is essential that the 3DTV supports a display mode where the input signal is shown directly on screen, without scaling (overscan) and other post-processing (which would destroy the stereo effect). On LG 3DTVs, you can set this display mode by labeling the input with "PC" (push the "Settings" button on the remote, then go to Input > HDMI1, push the red button with the single white dot and select the "PC" label). If your graphics card/notebook only has a DVI output, don't forget to buy a DVI->HDMI adapter and a HDMI cable. Finally, it is noteworthy that passive stereo screens have a certain viewing volume. On the LG 42LB620V, your head should be located about 2 meters away, aligned with the bottom of the screen (i.e. you should be sitting or the screen should be hanging high up on the wall). Inside the viewing volume, the 3D effect is crystal clear, but outside, there can be considerable ghosting. At least YASARA Model is required, click Window > Stereo > Interlaced to enable stereo. If the stereo is 'inside out', click Window > Stereo > Swap left and right.

High resolution 3D stereo with active shutter glasses is the next higher level, since it does not suffer from the reduced resolution of the passive screens above. The probably easiest solution with the best price/performance ratio is the Viewsonic V3D241wm shown on the right. The screen with a 24"/60cm diagonal has a resolution of 1920×1080 pixels and a non-reflective surface, it is thus well suited for everyday work. It functions with every operating system and every graphics card (nVIDIA/AMD) that can display quad-buffered stereo with 100 or 120Hz at a resolution of 1920×1080 pixels. The shutter glasses are included in the 350 EUR package. A slightly more expensive but also more commonly used and more flexible solution is nVIDIA's 3D Vision system, check the guidelines here and here. Other suppliers of 3D glasses are eDimensional and RealD.
Notes: Your graphics card must have a dual-link DVI connector and support quad buffered OpenGL stereo, a feature which is normally only available in workstation products like nVIDIA Quadro and AMD FireGL. You do not need the very expensive high-end Quadros with mini-DIN stereo connector, since the shutter glasses are supplied with the screen and plug into the screen with a cable, neither emitter nor batteries are required. Only one pair of glasses can be connected, so this system is for one person only. And since the monitor does not know the difference between left and right image, you may have to swap left and right in YASARA on startup. The aspect ratio of 16:9 is very movie-like, you may have to fiddle with your desktop settings to avoid windows that are too wide to read. The screen shows very little ghosting, which becomes noticeable mainly in the bottom 5cm. At least YASARA Model is required.

Recently also specialized 3D beamers, that previously cost above 10000 EUR, have finally become mainstream technology. You can now easily build your private molecular modeling showroom, projecting giant 3D views that measure several meters along the diagonal. The image on the right shows a 3D beamer from Viewsonic, costing around 500 EUR. The beamer projects the images for left and right eye alternatingly with 120 Hz. So you additionally need shutter glasses to separate the images, the probably best choice are glasses with DLP-link like the Viewsonic PGD-250 (~80 EUR) or the XPAND Edux3 (~80 EUR). An alternative with a less comfortable infrared emitter are the nuVisionGX glasses shown on the right (~200 EUR). Any beamer that is 3D-ready, features 'DLP-link' and supports a 120 Hz mode over VGA or DVI cable should work with YASARA, to see examples click here, then select 'Supported 3D projectors'.
Notes: Tests have been done in Linux, where you need to add a 120Hz modeline to your xorg.conf. Other operating systems work too if they allow you to choose a 120Hz video mode in their display settings. Additionally, your graphics card must support quad buffered OpenGL stereo, a feature which is normally only available in workstation products like nVIDIA Quadro and AMD FireGL. These cards often also have a mini-DIN connector for the shutter glasses, which is however not needed if you chose glasses with DLP-link (see above). The only disadvantage of DLP-link glasses is that you sometimes need to manually flip left and right image. At least YASARA Model is required to display stereo.

The Virtual Window is an autostereoscopic 19" LCD/TFT screen that allows you to see 3D without any additional glasses. Just press a button to switch between 3D and 2D mode. Order now from Dimension Technologies.
Notes: The Virtual Window provides a 3D button, that activates a filter which directs the odd pixel columns to the left eye, and the even pixel columns to the right eye. So the original resolution of 1280×1024 pixels is reduced to 640×1024 pixels per eye, leading to reduced text quality, just like the Zalman screen above. Since there are no glasses, the 3D view depends on your position and inverts if the head is moved too far. The Virtual Window requires at least YASARA Model and a video card that supports quad-buffered OpenGL stereo, e.g. NVIDIA Quadro cards.

Models@Home is a distributed computing environment that follows the spirit of the famous Seti@Home project, but is not tied to a specific application. Instead you can run all your favourite programs in parallel, without any need to modify or adapt them. The Models@Home screensaver allows to turn a heterogeneous Windows / Linux network into a uniform cluster.  At the CMBI , Models@Home is used for most protein modeling tasks, all YASARA force fields were developed with computer power provided by Models@Home. Models@Home is freely available including the source code.
Click here to download, click here for more information.