Alongside infiniSee 6 ‘Echo’ we release updates to our command line tools that explore and create Chemical Spaces. Computational and tech-savvy medicinal chemists receive several powerful augmentations to the software; these help fine-tuning search parameters to perform even more efficient screening campaigns. New to those features are the new SMARTS support and an easy “R-group search” within SpaceMACS as well as many others.
Detailed information can be found in the user guides of the respective command line tools (available as download and included in the tool package’s doc/ subfolders).
SpaceMACS 1.1
- SMARTS support for queries: It is now possible to specify SMARTS substructure language patterns as queries (via the --input option): Specify a SMARTS pattern directly as string enclosed by quotation marks, or specify a text file containing multiple line-separated SMARTS patterns. The text file must have the extension .sma or .smarts. As of today, recursive SMARTS definitions are not supported.
Mind that our “match images” (via --match-image-base-file option) cannot be generated for SMARTS queries.
[User guide: page 8] - New search type “R-group search”: Identifies compounds that contain the full chemical motif of the query with a defined substitution pattern and exit vector definitions.
(--search-type=0).
[User guide: pages 20-23] - New search type “MCS similarity”: Finds compounds that have a maximum common substructure and a comparable size to your query on the top ranks.
- (--search-type=3).
[User guide: pages 17-18] - Adjusted order of search types: New ordering of the different search types in a logical order from the strictest exact substructure matching with constraints (--search-type=0, R-group search) to the least strict MCS similarity matching (--search-type=3). Default is the MCS search with the MCS size as sorting criterion (--search-type=2).
[User guide: page 12] - New option “–min-similarity-threshold”: Sets a similarity threshold below which results are discarded. Only available for MCS similarity searches (--search-type=3).
[User guide: page 12] - More information in the match images: In addition to the highlighting of the MCS, the size of the MCS (MCS size = number of heavy atoms that are part of the MCS) and the proportion of the query and result covered by the MCS (coverage) are annotated.
[User guide: page 11] - Clearer console output: If you do not specify an output file, reduced output is written directly to the console. This now includes the rank, the MCS size or MCS similarity value (depending on the selected search type), the SMILES, and the name of the results.
[User guide: page 7] - Bugfix: MCS highlighting in match images was not always correct for results of library searches if the results contained the query motif multiple times.
FTrees 6.11
- Clearer console output: If you do not specify an output file, reduced output is written directly to the console. This now includes the rank, the Feature Tree similarity value, the SMILES and the name of the results.
[User guide: page 7]
SpaceLight 1.3
- New option “--expand-alternative-results“: Results are not de-duplicated. Identical results from different reactions/reagents or from different Chemical Spaces are written to the output.
[User guide: page 14] - Clearer console output: If you do not specify an output file, reduced output is written directly to the console. This now includes the rank, the fingerprint similarity value, the SMILES and the name of the results.
[User guide: page 8]
CoLibri 8.1
- SpaceLightDBCreator: Added new option “--protect-spaces“: The protection of the IP value in SpaceLight databases is now optional. If set, the name and chemical representation of the molecules and fragments is encrypted.
[User guide: page 20] - SpaceLightDBCreator: Added new option “--include-macrocycles“: Single rings with more than 9 ring atoms may be part of building blocks and can be formed by reactions.
[User guide: page 20] - Bugfix – FragSpaceMerger: Merging of single spaces failed if they contained certain cyclic fragments with a single atom as substituent.
- Bugfix – ReactionSynthesizer: Fixed a bug in space generation leading to artifacts in SpaceMACS and FTrees results because of incorrect name resolution.