infiniSee changelog

[2024-06-25]

• R group searches in Chemical Spaces: The Motif Matcher now supports R group searches in Chemical Spaces, which can be initiated using a new dedicated “[R]” run button.
  • For these searches, results will have a substituent with at least one heavy atom at the R position
  • Molecules containing R groups/atoms can be imported into the Motif Matcher through all existing methods and used directly as queries.
  • The eSeeSketch editor now allows the addition of R groups to molecules, simplifying the preparation of molecules for R group searches within infiniSee.
  • Queries containing R groups are now considered invalid in the Scaffold Hopper and Analog Hunter
• Distinct similarity analyses: Three distinct columns now display similarity metrics from the three search modes within the Analyzer Mode, enabling easier sorting and filtering.
  • This change eliminates the confusion caused by a single column containing multiple types of similarity values.
  • The column header tool tips now provide a more accurate and qualitative description of the corresponding similarity metrics.
  • The column names in Excel and CSV exports, as well as the SDF tags for these new columns, have been updated to align with the naming convention used within the infiniSee GUI.
• Introduction of ad hoc libraries: Results from a search mode can be saved within infiniSee as an ad hoc library to then be used as a search library in all (other) search modes.
  • The creation of ad hoc libraries is facilitated by a newly added button on the toolbar of the data tables.
  • An ad hoc library created is selected by default for the next search and is accessible under a special category within the list of Chemical Spaces and libraries.
  • Ad hoc libraries are only valid for an active session are not saved with the infiniSee project.
• Expansion of supported chemical elements: infiniSee now supports four new semi-metal elements: Germanium (Ge), Arsenic (As), Antimony (Sb), and Tellurium (Te), expanding the capability to design and search spaces for novel compounds incorporating these elements.
  • The eSeeSketch editor has been updated to support the creation or modification of molecules containing these newly added elements.
• Additional visualization possibilities
  • A new visualization type called "import source" has been introduced in the Analyzer Mode to display the distribution of molecules based on their import source.
  • Similar to existing visualization methods, molecules grouped by "import source" can be used as filter criteria.
• Easier reuse of queries: Any molecule entered into the query field of a search mode can now be transferred to another search mode via a right click action, regardless of whether a search has been conducted with that molecule.
  This changes the previous requirement that a search must have been conducted for the molecule to be transferred.
• Easier license status identification;Search modes that are unavailable due to a lack of license will display a red 'lock' icon on the mode switch.
  This proactive approach informs users of the license status before attempting to enter the mode, enhancing clarity.
• Miscellaneous improvements
  • Favorites and Annotations set within one BioSolveIT GUI application (infiniSee for example) can now be seamlessly read and displayed in another (SeeSAR for example), enabling cross-application access.
  • Note 1: The full functionality of this feature will be realized after the release of the next version of SeeSAR.
  • Note 2: starting with this release, the SDF tags for all outputs will no longer include the word 'INFINISEE'.

[2024-03-08]

• Introduction of the 'Motif Matcher': Completing the trinity of Chemical Space search methods, infiniSee has incorporated the Motif Matcher into its platform. This strategic integration enhances the repertoire of tools available for users seeking to explore the intricate landscapes of chemical compounds. Motif Matcher, powered by the SpaceMACS algorithm, delves into the combinatorial richness of Chemical Spaces, enabling the identification of compounds that contain specific substructures of interest.
  
  • Maximum common substructure (MCS) search: Retrieves compounds that share the highest overlap with your query compound. If an exact match is not present in the screened Chemical Space, infiniSee will fetch molecules in close proximity to the query compound that exhibit the largest connected substructure in common.
  • Exact substructure search: Retrieves compounds that feature a specific molecular motif, ignoring the rest of the molecule.
  • You can highlight parts of your query molecule to perform the respective search methods for the selected motif.
  Further details about Motif Matcher can be accessed via the following link.
• Supportive start screen: When initiating a new project, the updated start screen in infiniSee now assists you in choosing the perfect search mode. This intention-driven augmentation aims to guide newcomers effectively in accomplishing their objectives.
• Query compound transfer: After performing a search, query molecules can be moved to other modes by right-clicking on the structure.

[2023-10-26]

• Compound clustering with Bemis-Murcko scaffolds and Skeletons: The Bemis-Murcko scaffold generation methodology has been introduced in the Analyzer Mode enabling a quick means to simplify large datasets by abstracting the data to relationships between molecules and their core structures. Two types of representations are computed namely Bemis-Murcko scaffolds and skeletons.
  Scaffolds and skeletons can be generated both on individual molecules or on a group of checked molecules in the Analyzer Mode table:
  • On single molecules, right-click on the molecule entry and then click the corresponding scaffold/skeleton calculation option.
  • For multiple checked molecules, the newly introduced “Calculations for checked molecules” toolbar button is to be used and the appropriate option selected.
  Grouping molecules based on scaffolds or skeletons can be done in the Data Panel by choosing one among the multiple new options introduced under the “Visualization” dropdown menu.
  The information regarding Bemis-Murcko scaffolds and skeletons are also contained within the Excel, CSV, and SDF files exported from infiniSee.
• The grid view is now the default for scaffold, skeleton, and reagent visualizations.
• Single or multiple checked Scaffolds/Skeletons can be used as filters to narrow down that data to only those containing the particular scaffolds or skeletons.
  • On single entries, right-click on the scaffold/skeleton entry, and then click on the “Create filter” option, and finally confirm the filter parameters in the Filter Panel.
  • For multiple checked entries, clicking the filter button on the top left edge of the Data Panel, will select the checked entries as filter parameters. The setting of the filters based on the chosen entries is done as usual in the Filter Panel.
• Enhancements to the Analog Hunter: Analog Hunter searches now also generate query-result matching images in the 2D panel providing a visual and intuitive indication of similarity.
• Queries in the Analog Hunter can now contain macrocycles, and meaningful results will be delivered as long as the Chemical Space searched contains compounds with macrocycles. Note: The Chemical Spaces provided by BioSolveIT do not contain molecules with macrocycles, however if a user creates their own Space with macrocycles, then the corresponding results should be found. Furthermore, the Scaffold Hopper still cannot accept molecules with macrocycles as input.
  Molecules with macrocycles can also be loaded into the Analyzer Mode for further processing.
• Faster Scaffold Hopper and Analog Hunter searches: Searches in the Scaffold Hopper are now faster than before owing to an update of the underlying FTrees version from 6.9 to 6.10.
• Close-analog searching via the Analog Hunter is now significantly faster than before owing to an update of the SpaceLight algorithm from version from 1.1 to 1.2.
• New mode preview, mode selector behavior: A non-functional preview to a new search mode in infiniSee namely “Motif Matcher” for substructure searching in ultra-large combinatorial Chemical Spaces is available.
  The mode selector panel now dynamically resizes based on the user’s screen size or the size of the infiniSee window as set by the user.
• Vendor-specific molecule grouping and filtering: It is now possible to group molecules in the Analyzer that stem from either Scaffold Hopper or Analog Hunter searches, based on the corresponding Vendors using the “Molecules by Vendor” dropdown menu item in the Data Panel.
  The compound vendors can be used as filter criteria to narrow down the data in the Analyzer Mode to only those by the user-selected vendors.
• Grid view for reagents visualization: Besides the table view, in order to make efficient use of screening a Chemical Space, a grid view of the reagents in the Data Panel of the Analyzer Mode is introduced under the menu item “Molecules by reagent”.
• Enhanced control on calculations: Within the System Settings, a new “Calculation” option is introduced (similar to SeeSAR).
  Users can decide on whether they would like Bemis-Murcko scaffolds/skeletons and Optibrium properties to be automatically calculated or not under the following workflows:
  • Loading molecules from file
  • Adding molecules from a search mode to the Analyzer
• Improved interactions with histograms: Using histogram bins as filter criteria is now additionally possible with a right-click on the bin.
  Holding the SHIFT key and selecting two non-adjacent bins, selects all bins within the range to be used as filters.
• Keyboard shortcuts: Checking and unchecking entries in the Data Panel is now possible with the ALT+C keyboard shortcut. This shortcut works on both the table and grid views
• Changes to the behavior of notifications: From infiniSee version 5.1, only critical notifications (with the red background) will remain on the screen for the user to act on.
  All other non-critical notifications (orange background) and information (blue background) will collapse into the Message Center stack after being shown for a short period of time on screen.
• Miscellaneous changes:
  • The bubble-help pointing to the “Select a visualization” drop-down menu in the Data Panel in the Analyzer Mode is now shown only when there is data in the Analyzer table.
  • The parameters #stereo centers and #stereo bonds have been removed from the Analyzer Mode.
  • Query-result matching images generated by the Scaffold Hopper will not contain the global similarity displayed in the 2D panel.
  • An informative error message is shown if the user-selected location to save or create projects lacks write access.
  • The start-up screen now provides clear visual feedback when an invalid license file is dragged and dropped

[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 8^th 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.