|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.
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.
Double-click (on Windows) on the REAL Space Navigator icon on your desktop.
This will open a simplistic GUI — the REAL Space Navigator.
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:
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.
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.
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).
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.
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.
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.
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.
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.
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.
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.
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 chemical space. Please get in touch with us to learn more about this technology.