The KnowledgeSpace consists of 10,879 unique fragments derived from the combinatorial chemistry protocols. These fragments were approved by a medicinal chemist by eye and deemed to be of significant drug like nature. The properties of the fragments are mainly respect the Fragment Rule of 3 proposed originally by Astex, with filters applied for the properties of logP, donors and acceptors and molecular weight. Thus 90% of fragments have a molecular weight between 100-250 Daltons. Half of the molecules in the space contain at least 1 ring structure with approximately the remaining two quarters equally split between having no ring structure or 2 rings.

These ~11k fragments in the KnowledgeSpace can be combined in synthetically restricted ways using 488 unique linker types, with these link type constraints for compatibility and joining fragments in different ways there is the capability of potentially producing 11,725,417,388 virtual products that can actually be made! These searchable virtual products permit a vast improved coverage of chemical space in comparison to other screening solutions due to the potential diversity in the de novo compounds that can be screened. The KnowledgeSpace has been validated to retrieve known drugs and drug like molecules. See the details of some work in recent presentations where 1376 molecules from Drugbank were used as queries to create drug like molecules with FTrees-FS and how known CDK2 inhibitors were created de novo containing different CDK2 synthetic protocols with FlexNovo. The KnowledgeSpace is easily searched with our tools and has also been integrated into Pipeline Pilot^® and KNIME^® to enhance your existing pipelines and workflows. If you have any questions or would like access to the KnowledgeSpace please do write to us.

BioSolveIT have developed KNIME^® extensions for their most prominent virtual screening tools. KNIME^®, an Information Miner developed at Konstanz university is an open source project. KNIME^® is a free, modular and extendable data exploration platform to visually create data pipelines.

What does this mean for me you may be asking yourself?

Imagine, you wanted to filter a molecular database, screen it using docking then compare your best hits to your corporate compound database. This is a very easy workflow which can be 'plugged together' within minutes by dragging/dropping and connecting the so-called KNIME^® extensions in your work space area within KNIME^®.

The open source KNIME^® project contains some of the most advanced machine learning, clustering and chemoinformatics algorithms available, they have been created by multiple sources but can be all accessed and linked together under one roof – this powerful platform is shared throughout the community and can be potentially utilized by you!

Setting up our extensions is child's play: once the KNIME^® installer has finished its work, the installation of our BioSolveIT KNIME^® extensions is quick and straightforward. On examining the BioSolveIT extensions, Professor Michael Berthold, KNIME^®-creator and founder commented "Very impressive!". Also, as has been previously mentioned to our customers, for licensees of the respective tools, our KNIME^® extensions are free of charge. Following our mantra of one license = interface access galore for our customers ease of use! The BioSolveIT KNIME^® Extensions for FlexX/-SIS and FTrees can be downloaded now.

Within FlexNovo the user may either start from a known fragment binder or from alternative sources. For fragment growing one potential starting point is the results of a fragment crystallographic screen. Or alternatively compatible sub-structures can be matched and compatible molecules can be mapped to similar positions in the binding pocket of existing ligand binders. This provides a starting point to further explore the chemical environment of the binding pocket. If such information is lacking then the software can suggest a viable starting structure and design a novel compound in several molecular connecting steps following the initial placement.

Some preliminary results from FlexNovo were presented at the last Spring ACS Meeting in Salt Lake City, where the software was applied to the problem of finding novel molecular entities as starting structures in the quest for CDK2 inhibitors.

Interested researchers can request their evaluation copy here.

"I am very pleased with this new collaboration. This will further strengthen our market representation in Asia", says Dr. Christian Lemmen, CEO of BioSolveIT. CloudScientific has set the same goals as BioSolveIT has, serving the customer better by delivering unique and, when necessary, customized software that accelerates research due to its high level of scientific innovation and thus puts the user one or two steps ahead of its competitors.

As commented by Jiancheng Lin, "CloudScientific has developed rapidly since it was established, and by cooperating with BioSolveIT, we are able to significantly expand our portfolio with the best of breed technologies from BioSolveIT in drug discovery research to the benefit of our customers." All interested parties in evaluating or obtaining information about BioSolveIT software for China should contact Tao Huang at CloudScientific.

You can view previous topics of tips'n'tricks here. If you have any questions or know of any tips'n'tricks yourself that you would like to share with the BioSolveIT user community, we would appreciate your input at support@BioSolveIT.de.