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REAL Space Navigator: help

system requirements

hardware architecture: 64bit
main memory: at least 4GB
operating system Windows: tested on Windows 10
MacOS: tested on MacOS 10.13+
Linux: tested on openSUSE Leap 42.3

Depending on the size of the query molecule REAL Space Navigator may require a lot of memory. To be on the safe side — especially on smaller systems — we recommend saving and closing all open applications before you run the first test of the REAL Space Navigator.

installation

After the download, simply double-click (on Windows) to run the installer. Choose a location, where you have write permissions (e.g. the download-directory or your desktop). Make sure to check getting a shortcut-button with the REAL Space Navigator icon placed on your desktop. For other operating systems, follow the usual installation procedures.

simple usage

Double-click (on Windows) on the REAL Space Navigator icon on your desktop.

This will open a simplistic GUI — the REAL Space Navigator.

  1. Load a query molecule using on of the following ways:
    • Copy a molecule in your favorite drawing program and paste it in the Query panel using [Ctrl + V]
    • Drag&drop a molecule file into the Query panel
    • Use the load menu button or [Ctrl + O] to open a file browser
  2. Hit on the blue "Go!" button to execute the search in the REAL Space to retrieve molecules similar to the query.
  3. After a little wait (usually between 1 and 5 minutes depending on the size of your query molecule and compute power of your hardware), take a look at the results. At most 1000 results are provided, sorted by the distance of the similarity to the query molecule from the target similarity (cf. below). You may uncheck any results that you would like to dismiss right away. Note that multiple options are available with a click on the header of the checkbox-column.
  4. Finally "Save" the checked molecules to file (note that by default all molecules are checked at first). This export results in an SD file. You may further process your results or submit your export right away via email to Enamine to request a quote and thereby kick-off the purchasing process.

advanced features

In order to prepare REAL Space Navigator for the next search, simply hit on the "New" menu-button [Ctrl + N]. Alternatively, you may simply "Load" a new query just as described under the 1st step above (Note that MDL-Mol, Smiles, SDF and PDB are the supported formats. In case of multi-molecule files arbitrarily only the first molecule is loaded).

The search method implemented in the REAL Space Navigator is called FTrees. FTrees implements a fuzzy similarity search allowing you to find scaffold hops and remotely similar molecules. As the REAL Space is such a vast resource and as FTrees normally reports back only the most similar molecules, you may want to demand on purpose molecules with a lower similarity — thereby enhancing the chances of more scaffold hops, i.e. more surprises. You do this by shifting the slider in the query panel from right (more similar) to left (more surprises). The parameter controlled this way is called "target similarity", you will see its value upon a mouse-click on the slider.

The Results table shows molecules from the REAL Space with their FTrees similarity compared to the query molecule. By default the results are sorted by the distance of the similarity to the query molecule from the target similarity. With a click on the header of the similarity column you may sort the table according to the similarity. The first column of the table contains a checkbox for each molecule. By default they are all checked. With a click on the green "Save" button, all checked molecules are exported to file. A click on the checkbox-icon in the table header, reveals a menu with some useful functions (e.g. to uncheck all entries at once). Columns further to the right list a few simple molecule properties. A click on any table header sorts — if possible — by the contents of the respective column. Repeated clicks reverse the sort-order.

The menu bar in the header of the application provides some more functionality:

The footer of the application contains some basic status information and some more functionality:

license

REAL Space Navigator is equipped with a free 3-day trial license — valid upon download. The status may be checked with a click on the key-icon in the footer line. 24 hours before expiration of the license you will receive an expiration warning when you open the tool. After expiration, you may either download the tool again — or get in touch with us to inquire about a permanent license. If you receive a new license you may simply drop it in the license widget that can be accessed with a click on the key-icon.

REAL Space

The content (provided by Enamine Ltd.) is the world's largest collection of molecules available on demand. It is best described in this deck of slides. You may also be interested to watch this introductory video.

f.a.q.

You call this a giant "vendor catalog", but the molecules are just virtual — aren't they?

REAL Space is a collection of molecules, which Enamine will synthesize based on in-stock reagents and validated synthesis protocols. So they can be delivered — just like "real compounds" — in a very short time frame (usually within 3 weeks) and with high confidence (usually >80% success).

Are searches with REAL Space Navigator secure — or are my compounds transmitted?

Rest assured, no compound is transmitted by REAL Space Navigator. Despite its speed, it runs on your local machine and behind your firewall. This requires a local installation but allows you to search in complete safety.

What is the cost of a REAL Space Navigator license?

REAL Space Navigator is provided free of charge for a short time-frame (3 days after download). Once the license expired you may download the tool again and again — whenever you need it. If you are interested in a long-term license, please contact us — we provide these for a license fee.

Do I need a lot of compute power to run REAL Space Navigator?

REAL Space Navigator requires at least 4GB of main memory, but otherwise not much compute power. You may even run it on a laptop — given enough memory. Please read also about the system requirements at the beginning of this help page.

Sometimes I find loads of boring analogs only. How can I change that?

REAL Space Navigator reports what is available in the REAL Space. If the Space is very densely populated with analogs to your query molecule, we recommend to shift the slider above the query molecule from right (more similar) to left (more surprises). This will decrease the so-called target similarity and provide more distant results — hence more surprises.

Sometimes I find nothing really similar. Can I do something about it?

REAL Space Navigator reports what is available in the REAL Space. If the Space happens to be sparsely populated around your query molecule, the method cannot really do anything about it. But you can, let us know about these cases. We can then direct some effort into closing such gaps.

I am more used to substructure searching Can I do that in REAL Space?

REAL Space Navigator is based on the FTrees search method. Currently no other method can handle compound collections of this vast size. Please get in touch with us to learn more about future plans with this technology.

What is the scope of the search method, are there any limitations?

The search method within REAL Space Navigator called FTrees cannot handle macrocycles properly. FTrees is designed to work well with drug-size molecules — at most 100 heavy atoms are permissible. Similarly, at the other end of the scale, if your query molecule consists just of a single ring or less than 4 heavy atoms, you may not expect too differentiated a result list. In any of these cases, please contact us. We have special search methods available, to conduct such searches properly.

How does the REAL Space Navigator compare to other, similar resources?

First of all REAL Space Navigator is quite unique comprising the world-wide biggest collections of compounds available on demand. The search method — FTrees — working behind the scenes here is a pharmacophore-type search method. It is usually said to provide orthogonal results to other search methods. In other words it finds molecules of interest that other methods miss. If you have additional information about your target, e.g. a protein structure or the bound conformation of your current lead, we highly recommend you to use other methods such as docking, or 3D-alignment to post-process FTrees results thereby eliminating false positives from the admittedly fuzzy similarity searches.

Can I use it to search in other spaces or even plain compound collections?

REAL Space is hard-coded in the Navigator. However, FTrees may be obtained separately and be used with any input, both in terms of chemical spaces and in terms of traditional molecule libraries. Furthermore, you may obtain CoLibri, the tool used to create REAL Space and create your own chemistry space. Please get in touch with us to learn more about this technology.