Yasara structure

Interactively build small molecules in just seconds with a sophisticated builder that offers over 50 functional groups to choose from. Identify related structures in the PDB. 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. Bio-Prodict 3DM - The protein superfamily data integration platform. The polarized glasses ensure that the left eye sees only the odd pixel lines, while the right eye sees the even lines.

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YASARA - Yet Another Scientific Artificial Reality Application

Support for over 70 molecular fileformats based on OpenBabel. Homology modeling with 4 clicks and CASP approval. Gene fusion events are detected, where the target sequence spans more than one template molecule.

Align multiple proteins based on their structure or sequenceusing a variety of methods.

This includes all kinds of hetero-oligomers, e. The shutter glasses are included in the EUR package. Superpose structures and structure ensembles, calculate proper RMSDs minimized by flipping equivalent atoms.

Just press a button to switch between 3D and 2D mode. It is unfortunately not struchure free of side effects and has therefore been applied with increasing care over the past years.

After the mimimization and MD, xtructure can compare the docked structure with the calculated structure and the actual X-ray structure. In case of insertions and deletions, an indexed version of the PDB is used to determine the optimal loop anchor points and collect possible loop conformations. Calculate the electrostatic potential using Poisson-Boltzmann or PME methods, visualize the results as densities, contours or surfaces.

Passive 3DTVs use exactly the same principle as described above for passive 3D computer screens, so they will work with any operating structture and any graphics card, with YASARA running in window or fullscreen mode.

YASARA: A Tool to Obtain Structural Guidance in Biocatalytic Investigations.

A certain stage contains the features of all the previous stages, plus a number of additional functions to tackle a wider sstructure of scientific questions.

To speed things up, the MD simulation will be done without water molecules. Analyze and show cavities formed by these surfaces. Run simulations at the touch of a button even in the presence of ligands, thanks to yaasra automatic force field parameter assignment for the General Amber Force Field GAFF.

Perform twisted structural alignments, where the protein is bent and wound to maximize the number of structurally aligned residuesfor example to create sequence profiles for homology modeling Prediction and visualization of ion binding sites using valence scanning. Change distances, angles and dihedrals interactively.

Sincea touchable YASARA has been available for mobile devices, and in Aprilvirtual reality with head-tracking was released:. Create alternative views of the sceneand switch between them using tabs at the top.

Automatic correction of cis-peptide bonds sfructure wrong stereoisomeres for homology model refinement. YASARA View is available for free and contains all the functions you need to explore a macromolecular structure interactively.

Ray-tracing for publication quality graphics at strudture resolutions, interactively move the lightsource, adjust shadows.

YASARA: A Tool to Obtain Structural Guidance in Biocatalytic Investigations.

The beamer projects the images for left and right eye alternatingly with Hz. Build oligosaccharides interactivelywith stepwise energy minimization. Align small molecules like ligands automatically, by superposing them on the largest common fragment. Support for special input devices like SpaceBall.

Since there are no glasses, the 3D view depends on your position and inverts if the head is moved too far.

Without glasses, the screen behaves just like any other screen and can be used for everyday work. Stereoscopic 3D molecular modeling hardware has become easily affordable, so that entire classrooms can enjoy this unique experience.

During the past years specialized 3D beamersthat previously cost above EUR, have finally become mainstream technology. CASP evaluation results are available here. If the alignment is not certain, alternative high-scoring alignments are created using a stochastic approach[7], and models are built for all of them. Support for the latest GPU shader features like hardware tessellation, where the GPU increases yasaara geometric details of polygon meshes e. This is hardly noticeable when looking at molecules, but becomes apparent when looking at characters.

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