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 35 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.
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 the DTI virtual window . You can load up to 250 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.
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).
Key features:
- Cross-platform and easy installation: Windows and Linux in the same directory, run directly from USB stick.
- Photo-realistic molecular graphics: up to 35 times faster than other OpenGL based solutions, even the ribosome rotates smoothly in CPK mode.
- Parallel (orthographic) and perspective projection.
- Support for over 70 molecular fileformats (based on OpenBabel).
- 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, hydrogen bonds, labels, arrows.
- 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 calculate RMSDs.
- Measure distances, angles, dihedrals.
- 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.
- 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
- Fully immersive quad-buffered OpenGL stereo with shutter glasses and nVIDIA Quadro cards.
- Create the fanciest molecular animations with automatic rotations, movements, zooms, text in 3D letters, texture mapping of BMP and PNG images.
- Encode animations in MPEG format, paste them into Powerpoint presentations.
- Import OpenOffice Impress and Microsoft Powerpoint presentations, add molecular animations to the slides.
- Work with 250 structures at the same time, move them around independently.
- Extensive coordinate manipulation: center, join, transform, oligomerize.
- Analyze contacts, hydrogen bonds and protein secondary structure.
- 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.
- Build atoms, residues, peptide chains, terminal caps and mutate amino acids.
- Show and calculate Van der Waals, molecular and solvent accessible surfaces, distinguish between outer and inner surfaces, calculate volumes.
- 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.
- Prepare a simulation: clean proteins, predict pKas, assign protonation states, fill the simulation cell with water.
- Ultrafast (Assembly language) molecular dynamics simulations 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.
- Calculate energies, binding energies and solvation energies.
- Manipulate a simulation interactively: pull atoms or entire molecules around, fix and free atoms, add restraints, toggle force field terms.
- Show the electrostatic potential in the simulation cell, color surfaces accordingly.
- 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 charges.
- 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 etc.
- Read and write trajectories in SIM or XTC format.
YASARA Structure finally contains all the functions needed to compute and predict macromolecular structures. This includes modules for NMR structure determination, prediction of protein structure and function, docking and drug design. YASARA Structure will become available this year. You can easily upgrade from one of the other stages by paying just the price difference.
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