Just press a button to switch between 3D and 2D mode. You can move your molecules through 3D space using the Connexion 3D SpaceNavigator with six degrees of freedom. 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.
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CASP evaluation results are available here.
YASARA: A Tool to Obtain Structural Guidance in Biocatalytic Investigations.
Measure distances, angles and dihedrals between groups of atoms like helices or planar side-chains. If the alignment is yaeara certain, alternative high-scoring alignments are created using a stochastic approach, and models are built for all of them. With a diagonal of 42" cmtwo polarized 3D glasses and a price of EUR, this 3DTV is an excellent deal that will please your audience.
Identify cis-peptide bonds and wrong stereoisomeres.
Please contact for details and pricing information. This is hardly noticeable when looking at syructure, but becomes apparent when looking at characters. Knowledge-based loop modeler with a compressed index of the PDBpeptide segments spanning selected anchor residues can be located within a fraction of a second, while considering sequence and secondary structure preferences.
All features can be used with a virtual reality headset on Android. Create multiple interactive cut-planes to look inside surfaces and other objects.
Batch-processing of large data sets directly from the GUI graphical user interface. Create realistic 3D structures from nonsense, 1D or 2D moleculesand convert them back to 2D structural formulas. Change distances, angles and dihedrals interactively. Sincea touchable YASARA has been available for mobile devices, and in Aprilvirtual reality with head-tracking was released: Finally you can view a simulation of the complex in a waterbox run previously, and compare energies during the simulation.
An unrestrained high-resolution refinement with explicit solvent molecules is run, using the latest knowledge-based force fields. This includes many features you often miss: The tasks above are performed for all combinations of templates and alignments, per-residue yasarw indicators for the resulting models are determined.
As a bonus, you get YASARA's yasxra 3D engine, which is up to 10 times faster than what you usually know from OpenGLyou can load multiple structures at the same time, create publication-quality ray-traced images including labels, strjcture program your own macros and Python plugins.
Click here to order or get a quotationclick here for more details. If the homology is too remote to be detected by PSI-BLAST, the target is considered difficult and templates have to be provided manually for example using one of the many fold recognition servers on the web.
Accurate treatment of long-range electrostatic interactions with the Particle Mesh Ewald approach. Run simulations of membrane proteins at the touch of a button. Features with unique properties which you will not find in other programs are marked with orange buckyballs below. Create alternative views of the sceneand switch between them using tabs at the top. Using minimization and MD you will get a better picture of favourable interactions between ligand and receptor.
MM and MD in YASARA
This allows to validate for example protein-ligands interactions, an important aspect in drug design. It has a quite glossy surface, reflections can be a problem in bright rooms, but are hardly noticeable in somewhat darker 'molecular modeling caves'. Order now from Dimension Technologies. Record macros or write them with a text editor. Align small molecules like ligands automatically, by superposing them on the largest common fragment.
Loops can be optimized together with surrounding side-chains, considering all energy components including solvation. A graph of the side-chain rotamer network is built, dead-end elimination is used to find an initial rotamer solution in the context of a simple repulsive energy function.
YASARA Structure features a complete homology modeling module that fully automatically takes all the steps from an amino acid sequence to a refined high-resolution model using a CASP approved protocol. Store the results of your analysis in tables, import them in Excel. YASARA View is available for free and contains the basic functions you need to explore a macromolecular structure interactively, comparable to other molecule viewers.
The shutter glasses are included in the EUR package.