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BioSolveIT SeeSAR 5.0 Final
Windows Software | BioSolveIT SeeSAR 5.0 Final | 27.33 MB

SeeSAR is a software tool for interactive, visual compound prioritization as well as compound evolution. Structure-based design work ideally supports a multi-parameter optimization to maximize the likelihood of success, rather than affinity alone. Having the relevant parameters at hand in combination with real-time visual computer assistance in 3D is one of the strengths of SeeSAR.
Stimulating exploration with SeeSAR, we have embarked on persuing a new cheminformatics compute paradigm of "Propose & Validate" with these first four themes accomplished so far:
1. affinities:
We implemented sophisticated graphics to visualize atom-based affinity contributions; that allow for a rough estimate of the ΔS / ΔH -split of the Free Energy. (This is an ongoing co-development between BAYER, the University of Hamburg and BioSolveIT.)
2. phys-chem properties:
Relevant parameters are computed on-the-fly or imported to be taken into consideration throughout the design process.
3. torsional 'heat':
Torsional statistics analyses (developed between Hoffmann-LaRoche and the University of Hamburg); is readily available via intuitive color-coding.
4. 'explorable space':
A tight fit is the prerequisite for both, affinity and specificity. Therefore, as guidance for the user, efficient computation combined with refined graphics provides on-the-fly visualization of gaps in the binding interface and positions where a tighter fit is likely to be gained.

Whats New in version 5.0:
This new version brings together several new features designed to give you more control over how you interact with SeeSAR and to speed up browsing in 3D. This means that a new project version is necessary - but here you may find the new project recovery feature useful! Major new features include the new protein ligands, molecules and editor tables plus the editor itself has seen great improvements in user friendliness. Finally, don't miss the new editor feature for editing covalently bound molecules.

Neater molecule management with the new protein and molecules tabs
The molecules table has now been given its own tab and is complemented by a new protein tab. This currently contains the protein ligands table showing the ligands loaded from your PDB file, while the table in the molecules tab is the molecules table you are already familiar with - having all the features previously found in SeeSAR such as filtering, calculating binding affinity with Hyde, pose generation etc. The editor has also been given its own fully interactive table to show the results of your last edits. Read more in the description of the new editor features below.

Edit, browse, and edit again - and even edit covalently bound ligands
As promised we have now added more features for covalently bound ligands. In SeeSAR 5.0 you can edit covalently bounds ligands just like any other molecule or ligand. First add your ligand to the molecules table and then you can select it for editing. Once you are working in the editor, you can take the time to view the results of your edits complete with Hyde atom coloring in 3D. To go back to editing, simply click continue on the edit menu.

A new binding site definition for comparability and speed
While the tables in the two tabs have the same look and feel, there are some slight differences. The protein ligands table shows you the binding affinity for all ligands in their binding sites as loaded from the PDB. However, to calculate the binding affinity or generate poses for molecules in the molecules table, you must first define a unique binding site. This binding site will be used for all molecules in the table, making the comparison of molecules that lie within the binding site more accurate - with the added bonus of greatly accelerating browsing in 3D. Currently the binding site can be defined really simply by choosing any molecule in either table as a starting point. The binding site then remains valid for all molecules in the molecules table until you decide to change your definition. The new binding site definition means that the estimated binding affinities calculated with the previous version of SeeSAR will now be incompatible with the new version and so they must be re-calculated. But SeeSAR can help you recover older projects - read on to find out more!

Recover projects saved with the previous SeeSAR version
A major release includes major changes that mean older projects can no longer be loaded exactly as they were. However, SeeSAR now has new project recovery feature which will load as much data as possible from projects created with the previous version of SeeSAR. Any missing data can then be re-calculated with just a couple of clicks.
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