There are four different stages of YASARA for
Linux, Windows, Mac OS X and Android
, aimed at increasingly complicated fields of application. A certain stage contains the features of all the previous stages,
plus a number of additional functions to tackle a wider range of scientific questions.
Features with unique properties which you will not find in other programs are marked with orange buckyballs below.
- Molecular graphics and analysis, freely download now
- Everything above, plus molecular modeling
YASARA Dynamics - Everything above, plus molecular simulations
- Everything above, plus structure prediction and validation, docking, knowledge-based potentials
YASARA NMR Module
- NMR structure determination
YASARA/WHAT IF Twinset
- Extensive structure validation (PDBReports) and WHAT IF functions
Android tablets and smartphones that can run interactive MD simulations starting at
A stereoscopic molecular modeling lab for
250 EUR, and a cave for 700 EUR.
Read more about the philosophy behind YASARA
: None, please download the free YASARA View to verify that YASARA runs on your computer
(and please contact us if you encounter problems).
| ||Stage I: YASARA View - Free download |
| || |
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 (see benchmarks
), 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.
- 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: 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.
- 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
Click here for free download,
click here for screenshots, click here for a complete feature list
| ||Stage II: 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.
- 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.
- 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.
- 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.
- Support for special input devices like SpaceBall and P5 glove (currently Linux only).
- Unlimited undo/redo.
| ||Stage III: YASARA Dynamics
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 at twice the speed you know from other programs.
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).
- 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 (benchmarks) and energy minimizations in non-periodic or periodic & triclinic crystal cells.
- 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 or XTC format.
- Build oligosaccharides interactively, with stepwise energy minimization.
| ||Stage IV: YASARA Structure
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.
- 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.
| ||The WHAT IF / YASARA Twinset |
| || |
The Twinset is a customized joint-distribution of
WHAT IF and YASARA Dynamics (Linux and Windows,
not MacOSX) or YASARA Structure (Linux only). With over 2000 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 for academic use and costs 1500 € /
1950 $ for unlimited commercial use per building (this fee is waived if you own a group leader license of YASARA Dynamics or Structure).
In addition, you need 512MB RAM, 1GB of swap space and
licenses for YASARA Dynamics or Structure and
also WHAT IF
. Click here for WHAT IF license details
, and note that the academic WHAT IF version is now shareware. Customers in Austria have to add
To order the Twinset, just place a normal order for YASARA Dynamics or YASARA Structure
and then request the Twinset upgrade from , telling us your WHAT IF license number. If you already own YASARA,
email us your YASARA serial number and WHAT IF license number.
| || |
| ||The 3D Molecular Modeling Lab for
250 EUR |
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
Notes: The ZM-M220W has a resolution of
1680x1050 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 1680x525 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.
| ||High Resolution 3D Modeling for
350 EUR |
3D stereo with shutter glasses is the next higher level, since it does not suffer from the reduced resolution of the Zalman 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
1920x1080 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
1920x1080 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
3D Vision system, check the guidelines here
. Other suppliers of 3D glasses are eDimensional
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.
| ||The 3D Molecular Modeling Cave for
700 EUR |
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.