BioSolveIT infiniSee 5.1.0 | 47.7 mb

The Team BioSolveIT are proud to release Version 5.1 of the Chemical Space navigation platform infiniSee, named ‘Artemis’ is that gives easy and graphical access to searches in infinitely large chemical spaces of tangible molecules, and finds molecules based on a fuzzy pharmacophore-like similarity to an input query.

Bemis-Murcko Clustering: Molecular Scaffolds in infiniSee ‘Artemis’ 5.1 – Date: October 13, 2023
Vast Chemical Space Navigation: We are thrilled to share the launch of infiniSee ‘Artemis’ 5.1, which comes with numerous innovative enhancements designed to enhance the compound selection process. Among the standout additions in this update is a sleek Bemis-Murcko scaffold clustering within infiniSee’s Analyzer Mode.

Introducing Bemis-Murcko Clustering
A key element driving the compound selection process is the selection of a chemically diverse set of molecules to increase the chances of finding actives. Diversity within a set offers the added benefit that, ideally, multiple individual molecular scaffolds are discovered, which can serve as potential starting points for an optimization series.

The much requested introduction of Bemis-Murcko scaffold clustering augments this step: Given a set of compounds in the Analyzer Mode (e.g., infiniSee results from the Scaffold Hopper or the Analog Hunter Mode, individual molecule libraries, SMILES, …), entries can be categorized by molecular scaffolds and skeletons in the data visualization window. The frequency of calculated scaffolds or skeletons is given for each group — which in turn allows you to spot unique patterns, identify commonalities, and gain valuable insights into the composition and diversity of your compound dataset.

Now, data scientists and post-processing enthusiasts perk up your ears: Processed results in infiniSee’s Analyzer Mode will be tagged with the respective molecular scaffold and skeleton with a SMILES string which can be of great interest for any form of subsequent analysis, transformations and machine learning approaches. Simply export your results in a format of your choice (sdf, SMILES, xlsx, csv) to dive deeper into your compound prioritization.

Augmented Analog Hunter Result Representation

The colorful depiction helps users to understand the fingerprint alignment of the building block substructures to the query molecule to spot areas of high similarity and differences. Additionally to the global fingerprint similarity given for each molecule, individual local similarities of the substructure matching are presented in the 2D window. Ultimately, this feature also provides hints on the building block structures used in the synthesis of the result molecule.

These innovative features work in harmony with the existing components and tools within infiniSee, offering a seamless integration that will significantly elevate the efficiency and effectiveness of the compound management and selection procedures. Give it a try and test the Chemical Space navigation platform.

BioSolveIT infiniSee is that gives easy and graphical access to searches in infinitely large chemical spaces of tangible molecules, and finds molecules based on a fuzzy pharmacophore-like similarity to an input query.

Users can swiftly mine from 5 billion (5 x 109) Enamine REAL Space (not to be confused with the ten times smaller REAL database) — or use the company’s free KnowledgeSpace that is based on publically available building blocks and published reactions. The output can be either directly purchased from BioSolveIT’s partner Enamine; alternatively users can synthesize the results themselves with a very high likelihood due to the setup of the chemical spaces.

 

Classical library searches can certainly also be performed, these are processed quickly with parallel computing strategies that exploit multi-node architectures on standard computers and laptops.

 

Goodies include a forced match of user-selected subgroups; likewise very helpful is the 2D color-coding of molecular sketches that help the user understand the computed similarities. Results can be exported as SD files, remarkably with 3D coordinates on demand, or as CSV files for post-processing with a text editor. Queries may be masked to maintain IP safety.