infiniSee Help

If you want to use your own Chemical Space or use an updated version, open the 'System' dialog on the right-hand side of the toolbar followed by pressing the 'Search' button.


In the right window, under 'Installed locally' click on the 'Load Chemical Spaces from your file system' and select the compound collection to be screened (e.g. *.smi, *.sdf, *.space) from the respective folder.


Next, you load a query molecule and followed by the selection of the spaces. To do so, press the Space button, select the spaces of interest and hit the Start search button.


Now the search commences. Depending on the power of your PC and the size of the library or space, this may take anywhere from minutes to hours. We recommend you to start with a smaller library or one of our Chemical Spaces to get a sense for the search time.

Once the search is complete you get a results table and a visualization of any selected result. Use the check-boxes in the middle to mark any compound of interest for export.

After performing a search with infiniSee your results will be presented in a table. The column "Source" tells you the origin of the Chemical Space that contains your solution; the ID of the respective result molecule is shown in the "Name" column.
Compounds can be ordered by sending a quote request to the compound vendor with the following information:
Requested structures in SMILES or SD format, Compound ID (concatenated), and amount requested.

For compounds from Ambinter's AMBrosia Space, send your request to ambrosia@greenpharma.com.
For compounds from eMolecule's eXplore Space, send your request to explore@emolecules.com.
For compounds from Enamine's REAL Space, send your request to libraries@enamine.net.
For compounds from WuXi's GalaXi Space please send your request to contact@labnetwork.com.
For compounds from OTAVA's CHEMriya Space please send your request to info@otava.ca.
For compounds from Chemspace's Freedom Space please send your request to sales@chem-space.com.

For a lot of our users the safety of their data is of utmost importance. infiniSee runs locally on your computer, i.e. behind your firewall.

For any export of results may select to include the query that led to these results or mask the query. In case of the latter, neither the query, nor the similarity of a result to the query is exported. And in addition the sort order of the compounds is randomized.


Such an export may be used for external communication (e.g. with a compound vendor) without disclosing information about your proprietary data.

infiniSee can calculate and predict following parameters of a molecule that can be further used for filtering steps and compound assessment: HYDE-based (Lipophilic) ligand efficacy (LE/LLE), molecular weight, logP, total polar surface area (TPSA) of a compound, H-bonds, H-bond acceptors and donators, heavy atoms, aromatic rings, maximum ring size, total charge, and presence of covalent warheads. You can also calculcate and filter for following numbers: odd torsions, heavy atoms, (aromatic) rings, aromatic atoms, nitrogen and oxygen atoms, halogens, stereo centers, stereo bonds, and rotatble bonds. With this you can easily tailor your filters for particular compound features and
Furthermore, infiniSee supports the Optribrium expansion to predict a variety of important ADME parameters for further compound assessment:

ADME parameter
2C9 pKi	Cytochrome P450 CYP2C9 pKi prediction. Affinity prediction of the compound to bind at the enzyme involved in several metabolic drug pathways.
2D6 affinity category	Cytochrome P450 CYP2D6 classification. Compounds are predicted to be in one of four categories: ‘low’ for compounds with a pKi<5, ‘medium for compounds with a pKi between 5 and 6, ‘high for compounds with a pKi between 6 and 7, and ‘very high’ for compounds with a pKi>7.
BBB category	Classification of compounds into ‘+’-category if log([brain]:[blood])≥-0.5 and ‘-’category if log([brain]:[blood])<-0.5.
BBB log([brain]:[blood])	Logarithm of brain-blood partition coefficient of a compound. Can be used as indicator for CNS active compounds.
HIA category	Human intestinal absorption classification. Compound which are predicted to be absorbed ≥30% are classified with ‘+’, compounds which are predicted to be absorbed <30% are classified with ‘-’.
P-gp category	P-glycoprotein 1 (also known as multidrug resistance protein 1 (MDR1) and ATP-binding cassette sub-family B member 1 (ABCB1)) transport classification. Predicts if a compound is a substrate of P-gp.
PPB90 category	Plasma protein binding classification. Predicts a classification of ‘low’ for compounds which are <90% bound and high for compounds which are >90% bound.
hERG pIC50	Prediction of pIC50 values for inhibition of human Ether-a-go-go Related Gene (hERG) potassium channels expressed in mammalian cells.
logD	Logarithm of n-octanol-water partition coefficient (also known as n-octanol-water partition ratio) at fixed physiological pH 7.4. Used to describe the relationship between lipophilicity and hydrophilicity of an ionized compound.
logP	Logarithm of n-octanol-water partition coefficient. Used to describe the relationship between lipophilicity and hydrophilicity of a neutral compound.
logS	Logarithm of intrinsic aqueous solubility in µM for neutral compounds.
logS @ pH 7.4	Logarithm of intrinsic aqueous solubility at physiological pH 7.4 in µM for ionized compounds.

Our software is license key protected. To generate your license, we need the Host-ID of the machine on which the software shall run.
In case of a server license, we need the Host-ID of the server machine.

There are several options to determine the Host-ID:

Systemlog

1. Open the System settings in the top right and choose “Systemlog”
2. You find the Host-IDs when you scroll all the way down, and search for the line "Host-ID" a few lines above.
3. You can either send us the complete Systemlog (copy and paste it into an email) or reduce the copied content to the HostID(s)

License menu

1. Open the System setting in the top right and select "License"
2. Click on "Request license"
3. Choose "individual assistance" in the now open website and submit your machine ID.

System terminal/Commandline

1. Open a system terminal/commandline (Windows: cmd, Mac: Terminal)
2. Change to the directory of the software executable
3. Call the app with --license-info, e.g. "seesar --license-info" or “infinisee --license-info”
4. Send us the complete output of this call

Follow these steps to manually enter a license file:

• Click on the System settings icon in the top right corner.
• Click the key icon (License) to open the license management interface.
• Select the license file or drag&drop it in this window.

If the license key is valid, you will see a green checkmark animation, and the license period will be updated in the green info line above.
Alternatively, you can place the license file into the directory of the software executable.
In case you want to add or update a server (floating) license file, please check the corresponding "server license" FAQ entry.

Our software is license key protected. A license can either be bound to a single node or to a dedicated license server.

A server license (als called "floating license") allows a flexible administration and usage as it is hosted by a server and distributed to compute clients on demand. Such a server may manage the license requests for hundreds or thousands of software clients.

How to set up the license server

1. First, please download the BioSolveIT flexlm package from our download page. Select the suitable package corresponding to your operating system.
2. Login to the computer, where you want to run the license server. Flexera Software strongly discourages running the license servers with elevated privileges. However, to install the license server as a system service, you might need elevated privileges during installation.
3. Extract the package on the license server computer.
4. Follow the installation notes in the chapter License Server Manager “lmadmin” in package file license /doc/fnp_LicAdmin.pdf
5. Copy the BIOSOLVE vendor daemon from the package directory license/bin to the new lmadmin installation directory. On linux, make sure that BIOSOLVE has executable rights - if in doubt, just execute chmod +x BIOSOLVE.

Making the server license available to local software installations
When you have fed the server with the license file, you have different options to make the license available to local software installations.
No matter which option you choose, if your license needs to be renewed, you only have to feed the license server with the updated file. The local installations don’t need the license again.

1. Installation directory
   • Just copy the license file into the directory of the software application, right beside the executable.
   • If you are using non-standard ports for the license server communication, you have to enter these ports into the license file.
2. Environment variable
   • Set the environment variable BIOSOLVE_LICENSE_FILE to point to the server name prepended by "@", e.g. BIOSOLVE_LICENSE_FILE=@my_server
   • If you are using non-standard ports, you have to specify the port number in front of "@", e.g. BIOSOLVE_LICENSE_FILE=12345@my_server

To find out why your license is not working, we need your help:
Please send us the systemlog (open the System settings in the top right, then choose Systemlog). Also, screenshots may be helpful, and errors/warnings in the exact wording.

The most frequent issues are:

• cannot connect to license server — check:
  • firewall and DNS configuration, any blocked ports?
• the key cannot be found - check:
  • key expiration (open the System settings in the top right, then choose License)
  • is the “.lic” file extension still there or has the mailer modified the file?
  • old license keys have to be removed
    • go to the software directory and delete outdated or invalid licenses files
    • if you are unsure about the software directory, look into the Systemlog (open the System settings in the top right and choose “Systemlog”, then scroll all the way down)

Important note: Every mode of infiniSee requires a valid license. To check if your license if valid for the mode go to the infiniSee interface and click on 'System' → 'License'. The duration and validity of your licenses is shown on the left.