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infiniSee is your Chemical Space navigation platform. Based on similarity, infiniSee finds molecules of interest in screening libraries or Chemical Spaces of almost infinite size. Given a template or query molecule, infiniSee returns unexpectedly similar molecules.
Let’s start with a thought experiment: If you fill an Olympic-size swimming pool with sand, you need a volume equal to approximately 10,000,000 cups of coffee. This volume, in turn, contains approximately 1013 grains of sand. Now, think of these individual grains of sand to represent possible drug candidates and you are looking for the one golden molecule. High-throughput virtual screening (HTVS) usually involves around five to ten millions of compounds which would be the same as looking for one specific grain in five to ten cups of sand. But who can guarantee that the perfect molecule is in one of the 5-10 cups you take from the pool? Chances at best are 1 in a million... Wouldn’t it be better and more promising if you can search in the whole pool or even thousands of them?
This is what infiniSee and Chemical Spaces are all about.
Find hidden similarities
With infiniSee you can finally compare apples and oranges. The underlying concept of infiniSee is strikingly easy: instead of searching already “assembled” molecules, we instead perform a combinatorial build-up of compounds from “fragments”. Sources of fragments can be either combinatorial libraries or any fragment-generating procedure. InfiniSee opens the possibility to screen billions of compounds through its similarity search technology by navigating vast Chemical Spaces and searching for distant neighbors of a query molecule. Results will be delivered within typically less than a minute on a standard laptop. Optionally you can request fuzzy pharmacophores to increase the diversity of scaffolds or define important molecular structures to be present in the hits.
Your molecule can be anywhere
The ingenious twist of infiniSee is the possibility of searching not only in colossal Chemical Spaces, but the ability to also comb through spaces of different origins. The number of identical structures in sets from different spaces was found to be extremely low (Lessel et al. 2019) due to the design and setup of the spaces, as well as the diversity of the employed building blocks. No matter how big your in-house library and no matter how many compounds you acquire to add to it, it will only be a tiny fraction of what your chemists are capable of synthesizing. Involving distinct Chemical Spaces increases your chances of finding accessible molecules you would have missed otherwise.
Create your own Chemical Space
Sometimes the perfect solution is within reach in your own compound library without realization. You can design your own Chemical Space with your accumulated, in-house knowledge and resources. Reactions and building blocks can be defined to create massive numbers of virtual compounds. Multiple big pharma companies built their own, in-house Chemical Spaces to search for scaffold alternatives to reduce costs and time.
Five reasons for infiniSee
infiniSee stands second to none when it comes to speed. Navigate through Chemical Spaces of size 1014 molecules within minutes on standard hardware.
#2 Accessible results
Search in commercial databases, like GalaXi™ or REALSpace™, and find purchasable compounds which are delivered to your table within a few weeks.
#3 Size matters
infiniSee is the only tool that navigates Chemical Spaces of almost infinite size. Increase the chances of finding your perfect molecule by expanding your hunting grounds.
#4 Break patents
Discover new scaffolds of approved drugs and patented molecules with only a few clicks. infiniSee provides you with distant yet related molecules.
#5 Safe use for everybody
infiniSee works on almost every computer. It requires only modest hardware while searching these giant compound resources in complete safety behind your firewall. Its graphical interface is intuitive for novices and experts alike.
infiniSee opens the possibility to screen billions of compounds through its similarity search technology. Search in one of our partners’ Chemical Spaces to obtain commercially available compounds (GalaXi™, CHEMriya™ and REAL Space™) or literature-based virtual Chemical Space with high likelihood of synthetic accessibility (KnowledgeSpace™).
Desired compounds of our partners can be purchased and delivered to your table within weeks.
We are proud to introduce CHEMriya™ - OTAVA's on-demand Chemical Space. The first release of the CHEMriya Space contains 11 billion accessible molecules, based on 30 thousand building blocks and 44 in-house reactions. Several multi-component and ring-closure reactions provide a vast chemical diversity with a broad range of molecular scaffolds. As every Chemical Space is based on in-house knowledge and ressources, CHEMriya will further expand the search horizon of infiniSee, allowing you to search in new areas of tangible molecules. CHEMriya is featured in the latest version of infiniSee.
In partnership with Enamine Ltd. we built the world's largest collection of commercially available compounds, almost 19 billion molecules. We coded the Enamine synthesis protocols and in stock starting materials as a searchable Chemical Space using our CoLibri technology. REAL Space™ allows for efficient hit exploration, from finding previously unknown analogs to scaffold hopping. The Chemical Space is based on 160 Enamine synthesis protocols, 123,138 reagents, and 171,912 added building blocks. It provides an escape from availability bias of current stock screening collections towards intellectual property free areas.
The latest update of this Chemical Space now covers over 2 billion tangible molecules. In close collaboration with WuXi LabNetwork we created a novel Chemical Space ready for you to download and search. This space contains a lot of unique chemical intellectual property for your research, and compounds can be created on demand upon request with WuXi. GalaXi™ has been shaped from WuXi LabNetwork’s building blocks and reaction schemes that have been properly checked to deliver high quality results. High quality processing has been ensured using our CoLibri software.
KnowledgeSpace™ is comprised of more than one hundred literature reactions including ring-closures, coupling, substitutions, and multi-component reactions. The result is a literature-based virtual Chemical Space covering hundreds of billions of virtual products with high likelihood of synthetic accessibility. This space is ready for searching but can also serve as a blueprint for customization, capitalizing on your proprietary building blocks and chemistry protocols.
Synthetic access is the key to success in practically all pharmaceutical research projects. What can be made – easily enough – decides in the end what is actually made. CoLibri is a toolkit for Chemical Space exploration that transforms synthetic know-how into a Chemical Space, constituting huge numbers of virtual but synthetically accesible compounds.
Download CoLibri 6.1.1 for your operating system:
Get your CoLibri license:
Smart and user-friendly: infiniSee 2.5 features some additional perks to support Chemical Space navigators on their search for compounds. Our partners' Vendor business cards deposited in infiniSee. With this you have convenient access to all the information to get in contact with our partners for compound ordering. Furthermore, the Chemical Spaces are now listed with their respective release date. You will be informed by infiniSee if the Chemical Space you are searching in has a newer version available.
For older versions please visit here
Let’s compare Chemical Spaces to sauerkraut. The concept of fermented cabbage exists in many world cuisines; kimchi in Korea, kapusta kiszona in Poland, Cutrido in El Salvador. Although they follow similar preparation steps, the taste varies greatly due to the local ingredients used. Chemical Spaces behave alike: the knowledge and building blocks used to build up the Chemical Space differ between companies and methods involved. The overlaps between two Chemical Spaces can be surprisingly miniscule (Lessel et al. 2019
By searching in several Chemical Spaces you maximize your success rate to find a promising molecule.
The first thing about the results obtained with infiniSee from a chemist's point of view is that the molecules are aligned. This means the chemist can understand why the molecules are awarded a certain similarity. Also, the fuzzyness of the descriptor makes it ideal for finding scaffold hops.
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 Enamine's REAL Space, send your request to firstname.lastname@example.org
For compounds from WuXi's GalaXi Space please send your request to email@example.com
For compounds from OTAVA's CHEMriya Space please send your request to firstname.lastname@example.org
Follow these steps to manually enter a license file:
1. Click on the System settings icon in the top right corner.
2. Click the key icon (License) to open the license management interface.
3. Select the license file or drag&drop it in this window.
If the license key is valid, you will see a green check mark 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
Making the server license available to local software installations
- First, please download the BioSolveIT flexlm package from our download page. Select the suitable package corresponding to your operating system.
- 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.
- Extract the package on the license server computer.
- Follow the installation notes in the chapter License Server Manager “lmadmin” in package file license /doc/fnp_LicAdmin.pdf
- 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.
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.
- 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.
- 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
o go to the software directory and delete outdated or invalid licenses files
o 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)
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:
- Open the System settings in the top right and choose “Systemlog”
- You find the Host-IDs when you scroll all the way down, and search for the line "Host-ID" a few lines above.
- You can either send us the complete Systemlog (copy and paste it into an email) or reduce the copied content to the HostID(s)
- Open the System setting in the top right and select "License"
- Click on "Request license"
- Choose "individual assistance" in the now open website and submit your machine ID.
- Open a system terminal/commandline (Windows: cmd, Mac: Terminal)
- Change to the directory of the software executable
- Call the app with --license-info, e.g. "seesar --license-info" or “infinisee --license-info”
- Send us the complete output of this call
Any usage with a graphical user interface requires a local graphics card, i.e., a local computer. This can therefore not work from remote.
Commandline and KNIME runs however can be triggered from remote.
Please contact us if you need to work from home during the Corona pandemic.
- RAM: 8GB would be good, anything beyond is better.
- CPU: Our tools are not very hungry — yet they profit from multiple CPUs, because they have parallelized algorithms implemented. If in doubt rather choose more slower CPUs than one faster one.
- Graphics: It is important to know that a local graphics card is mandatory for infiniSee and SeeSAR.
Update to the latest driver, and check — even if Windows tells you that you are up-to-date. Lenovo and other computers with onboard graphics, please navigate to this link to check
if there is a newer driver available for you.
Couldn’t find what you are looking for?
Visit our elaborative FAQ section or the first aid section
Feature Trees (short: FTrees) is a highly efficient software tool for pharmacophore-style similarity searching, facilitating virtual HTS. The Feature Tree descriptor captures a molecule’s overall topology and its pharmacophore properties. The similarity of two such descriptors is based on an alignment (shown above by the color-coding of related functional groups).
Find out more about FTrees here
Recent success stories
- Warr, W. Report on an NIH Workshop on Ultralarge Chemistry Databases. ChemRxiv. 2021.
- Namasivayam, V.; Silbermann, K.; Pahnke, J.; Wiese, M.; Stefan, S.M. Scaffold Fragmentation and Substructure Hopping Reveal Potential, Robustness, and Limits of Computer-Aided Pattern Analysis (C@PA). Comput. Struct. Biotechnol. J. 2021.
- Salari-jazi, A.; Mahnam, K.; Sadeghi, P.; Damavandi, M. S.; Faghri, J. Discovery of Potential Inhibitors against New Delhi Metallo-β-Lactamase-1 from Natural Compounds: In Silico-Based Methods. Sci. Rep. 2021, 11 (1), 1–20.
Download infiniSee 2.5.1 for your operating system:
Get your license:
How to cite
In publications please cite infiniSee with the respective version number as follows:
infiniSee version 2.5.1; BioSolveIT GmbH, Sankt Augustin, Germany, 2021, www.biosolveit.de/infiniSee