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infiniSee changelog

[2023-03-08]
  • Introduction of the 'Analog Hunter': The newly added mode Analog Hunter opens the door to searching for close analogs based on molecular fingerprints in massive combinatorial Chemical Spaces using the SpaceLight method under the hood.
    infiniSee 'Artemis' applies the well-known ECFP4 fingerprint as metric in the Analog Hunter. The “whole-molecule-similarity” is shown as the similarity score.
    Further details on infiniSee 'Artemis' and the novel SpaceLight algorithm can be found here and here, respectively.
    Important note: The Analog Hunter will only work with the newest Chemical Spaces (compatible with SpaceLight 1.1). SpaceLight 1.0 Chemical Spaces will not deliver any results. Therefore, please download the latest versions of the Chemical Spaces (as of March 8th 2023).
  • FTrees is now the 'Scaffold Hopper': The FTrees search mode is now called 'Scaffold Hopper'. The remote service execution for FTrees is not a separate mode anymore, but the Scaffold Hopper mode switch can be toggled to choose between local and remote execution of FTrees searches by hovering over the button from left to right.
  • Adjusted Chemical Space management: Starting with infiniSee 'Artemis', Chemical Spaces are no longer embedded in the download package of infiniSee. Users have to download the latest Chemical Spaces from the improved 'Search' dialog within the System Settings in infiniSee. As always, Chemical Spaces can also be loaded and used from your local machine. The possibility of downloading the Chemical Spaces from our website still persists.
    You will be warned by infiniSee if a particular Chemical Space loaded by the user is not suitable to run Analog Hunter searches.
  • When updates to Chemical Spaces are available, you will no longer have to update infiniSee, but will be persistently notified (within infiniSee) from the first tool start after an update is available. The notification will also direct you to go to the System Settings > Search, and install the available updates.
  • Enhancements to the Analyzer: The Analyzer now has a new layout with the introduction of a separate data visualization panel. Further, the Analyzer will now be the default mode in infiniSee when you choose to start a new project from the start screen.
    Data in the Analyzer table can be analyzed with the help of histograms. All available properties can be plotted and visualized.
    Individual histograms bars can be used as filters. The data range contained within the bin are used as the filter ranges.
    When the data in the table is from Scaffold Hopper or Analog Hunter searches, the frequency of occurrence of specific reagents that make up the search results can be visualized by horizontal columns.
    Individual reagent names can directly be used as filters from the data visualization panel.
    The Analyzer contains only a single column named 'Similarity' which will contain the Similarity scores from both the Scaffold Hopper and the Analog Hunter.
  • Proceed with your last project: You can start to "continue working on their last used projects" from the start screen. So far this was only possible in SeeSAR.
  • Changes to license handling: All users with server licenses must update to the new Flexlm license libs 11.19.2.
    Each search mode in infiniSee will now be served only with valid 'module licenses'.
  • Improved license dialog: The 'License' option in the System Settings has undergone a facelift. You can, now from the get go, find out which modes you have licensed, and which modes are blocked and require a license for usage. Additionally, you will learn about the duration of the validity of the individual licenses.
  • User warning during remote usage of Scaffold Hopper: Scaffold Hopper remote users will be warned when their server connection is insecure. Further, they will be warned if the version of FTrees between the local infiniSee installation and on the remote server varies, thereby reducing the chances of inconsistent results.
  • Novel keyboard shortcuts: Commonly used table actions now have keyboard shortcuts, applicable across all modes.
    Check molecule - ALT+C
    Mark as favorite - ALT+F
  • Checked molecules indicator: When molecules are 'checked' on any table, an additional indicator on the total number of molecules currently checked is shown on the table header. This prevents accidental deletion/moving of molecules that you might have checked at a different part of the table beyond the current view.
  • Chemistry model changes: infiniSee received a major update of protomer and protonation states generation as well as optimization of parametrization of hit lists length and filter criteria for FTrees space search.
  • Augmented notification system: The way notifications are delivered in infiniSee has significantly changed, ensuring that you do not miss important notifications. There are fundamentally two kinds of notifications that are shown to users: (a) Infos (blue background), and (b) Errors/warnings (red or orange background).
    Errors and warnings remain on the screen and have to be explicitly closed by the user.
    There is an indication on the number of messages available in the Message Center.
    Within the Message Center, you now has the option to either 'clear all infos', or 'clear all messages'.
  • The 'What’s New' bullhorn-icon will show a 'notification indicator' to either indicate the availability of a new infiniSee version, or if the user has not clicked on this button to read the changelog even once.
  • The start screen will not contain the 'What's New' slides anymore, but a direct link to the changelog will be available via the new bullhorn-icon on the top right in infiniSee. In this way all changes can be systematically documented on the website, and the user has just this one place to be concerned about if they want to learn what’s new!
[2022-12-07]
  • REAL Space Update: Now featuring 33,939,091,721 virtual products based on 165 reactions, 104,140 reagents, and 185,636 additional building blocks.
  • eXplore Update: Now featuring 7,030,188,488,107 virtual products based on 43 reactions and eMolecules building blocks.
[2022-09-15]
  • Introduction of eXplore: Created in collaboration with eMolecules, the first version of the eXplore Space features 2.8 trillion compounds for users to search in. Users have the option to purchase the building blocks and perform the synthesis of the compounds themselves or to request eMolecules to do the synthesis. The curation of the building blocks allows shipping of those within few business days. 40 robust chemical reactions that can be performed in almost every lab in one to two steps were involved in the creation of the Chemical Space.
    We have prepared a cookbook-themed guide with insights on the chemistry behind the largest commercial Chemical Space so far which can be accessed here (PDF).
    Further details on eXplore can be accessed on its eMolecules website.
  • Freedom Space Update: The Freedom Space now features 1.8 x 108 entries. The required building blocks can be purchased from Chemspace.
[2022-07-27]
  • REAL Space Update: Now featuring 31,612,189,569 virtual products based on 165 reactions, 100,526 reagents, and 182,381 additional building blocks.
[2022-05-06]
  • Analyzer Mode
    The new inherent part of infiniSee is the Analyzer Mode for pooling molecule sets. This covers search results of infiniSee as well as any external sources (e.g. sd files, SMILES). Individual molecules and groups can be transferred from Local host & Web service to calculate compound properties (e.g. number of hydrogen bond donors/acceptors, aromatic rings, molecular weight, logP, TPSA, and many more). Molecules in the Analyzer can be linked back to their search queries as long as the search still exists in infiniSee (right click on molecule in table to show the corresponding search). Furthermore, users can conveniently use molecules from the Analyzer Mode as query molecules in the search modes.
  • Molecule filtering
    Within the Analyzer Mode users can apply filters to narrow down the displayed compound for further assessment.
  • Building block annotations
    infiniSee search results now contain the building blocks used in the synthesis of the compound. Those can be added to the table by checking the 'Reagent' tags.
  • ADME properties by Optibrium
    Pharmacokinetic and pharmacological properties are an important factor during compound evaluation. Therefore, we added the possibility to calculate important ADME properties in infiniSee for all compounds loaded into the Analyzer Mode. Usage requires the optional StarDrop module by Optibrium.
  • Histogram plotting
    Users can plot histograms of calculated physicochemical properties within the Analyzer Mode to assess the distribution and quality of the loaded molecule set.
  • Over 50 billion accessible compounds
    Pandora is accompanied by the largest Chemical Space updates so far resulting in over 50 billion make-on-demand compounds from four different compound suppliers. The huge expansions of the REAL Space and GalaXi, alongside the introduction of the forth Chemical Space by Chemspace, the Freedom Space, open the doors to novel scaffolds and functionalities within molecules. Profit from this major update and load your favorite molecule into infiniSee to screen those huge molecule collections to discover novel surprises that may accelerate your drug discovery projects.
  • Introduction of Freedom Space by Chemspace
    We are proud to announce the addition of a forth novel make-on-demand Chemical Space: The Freedom Space by Chemspace. In his first version the Freedom Space contains 1.5 x 108 molecule entries that can be ordered either as already synthesized final products or as seperate building blocks that can conveniently be used for synthesis in your own labs.
  • REAL Space Update: Now featuring 29 billion compounds.
  • GalaXi Update: Now featuring 12 billion compounds.
  • A warning is displayed when the project size almost exhaust the tmp disk space.
  • Users get a warning that for molecules with linker (R) atoms, Optibrium properties cannot be calculated.
[2022-02-12]
  • REAL Space Update with two billion novel compounds. The Chemical Space now features over 23 billion entries.
[2022-01-20]
  • CHEMriya Update with novel reactions.
  • Compounds can be marked as favorites in the search results. The favorites column can also be sorted for your tagged molecules.
  • Users can add annotations to molecules.
  • Query compound's name can now be edited by double-clicking on the name.
  • The export of molecules from infiniSee is now enabled by a button placed right above the results table. The "per-source" export functionality has been enhanced to include a choice between SDF, CSV or SMILES formats.
  • Your checked molecules can now be conveniently copied as SMILES strings to the clipboard and external applications.
[2021-10-14]
  • REAL Space update featuring novel reactions and over one billion added compounds is introduced to infiniSee.
[2021-09-23]
With the release of infiniSee 3.1 we have improved and refined the Andromeda version to make Chemical Space exploration even more liberating and exciting.
  • Introduction of eSeeSketch
    Users have now the possibility to draw molecules from scratch in infiniSee itself without the need of external drawing software or SMILES. Created molecules can subsequently be used as query molecules for searches within infiniSee. Furthermore, if you find any interesting results from your Chemical Space search you can directly modify those with eSeeSketch. With this we provide users with the option to make small modifications on the molecule (e.g. substitution pattern, positions of heavy atoms within ring systems) for subsequent investigation of analogs.
    You may notice that no stereochemistry options are available in eSeeSketch. Since FTrees does not take into account any stereochemistry of a molecule (e.g. R/S, cis/trans) no implicit information during sketching is required.
  • Convenient export of molecules
    Any molecule in the results table can be exported to other applications as SMILES. With this you can select individual entries and transfer them to external applications for follow-up investigation and evaluation.
  • Drag-and-drop within infiniSee
    Interesting compounds from the results table can now be dragged with right-click into the query window of infiniSee. Sometimes a result molecule features interesting properties and structural elements that creates interest to explore related molecules. Now you can easily focus your exploration on specific areas of the Chemical Spaces by directly interacting with the results.
[2021-07-26]
infiniSee 3 (codename: Andromeda) aims to support you in your drug discovery projects.
  • Search history
    Each of your Chemical Spaces seaches is now stored within infiniSee with the applied seach parameters. Now you can easily compare your discoveries of different sources right ahead in the GUI. The result summary informs you for how many compounds you searched, which pharmacophore constraints were applied, who has started this query, and even how fast infiniSee handled the search in zillions of compounds.
  • Projects
    You can now save your sessions as so called 'projects'. If you want to pick up on from a past session, you can load the project and continue your work.
  • Update of the REAL Space
    Enamine's Chemical Space has received an update which is already conveniently included in infiniSee 3.0. Browse in the world's largest on-demand Chemical Space to discover relatives to your query molecule.
[2021-05-29]
Smart and user-friendly: infiniSee 2.5 features some additional perks to support Chemical Space navigators on their search for compounds.
  • 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.
  • The Chemical Spaces are now listed with their respective release date. Furthermore, you will be informed by infiniSee if the Chemical Space you are searching in has a newer version available.
[2021-05-07]
  • The latest update of infiniSee introduces OTAVA's on-demand CHEMriya™ Space with over 11 billion molecules.
  • Furthermore, we included a feature to export multiple files based per search source. With this you can easily track the origin of your results.
[2021-04-23]
  • Update of Enamine's on-demand REAL Space, featuring 19 billion molecules.
[2021-03-05]
  • Update of Enamine's on-demand REAL Space, featuring 17.6 billion molecules.
[2021-03-05]
  • Available BioSolveIT and partner Chemical Spaces are now automatically part of the infiniSee package.