CzeekD is a de novo compound design system utilizing optimization algorithms, developed by Kyoto Constella Technologies. Designed as a tool to support medicinal chemists, it enables design of new compounds, as well as side chain modifications in initial structures. It fully exploits the novel Chemical Genomics-Based Virtual Screening (CGBVS) technology to screen and select the best potential target compounds.

CzeekD enables the user to set a core structure in combination with one or more provided fragment libraries to create compounds based on one or more target proteins. These compounds are evaluated based on the CGBVS technology leading to the creation of a library of high scoring compounds.

Kyoto-Constella recently released the CzeekD Open Site: users can use our de novo compound design system CzeekD with ChEMBL Models free of charge.
Please follow the link to CzeekD on K-C website to access the Open Site.

Some of its features:

  • Fragment-based Compound Design: generates virtual compounds by connecting fragments based on a synthesis frame. The use of RECAP (Retrosynthetic Combinatorial Analysis Procedure) results in the creation of virtual compound libraries containing compounds that are synthetically accessible. CzeekD also allows the use of commercially available building block databases (combichem building blocks, intermediates, etc.) as fragment libraries.
  • Efficiently searches chemical space through the use of optimization algorithms: it has been said that, theoretically, the total number of compounds that can compose a chemical space is over 1060. Particle Swarm Optimization (PSO), which is the optimization tool employed in CzeekD, enables the efficient search of such large chemical space.
  • Creation of various libraries using CGBVS as fitness function: the use of CGBVS method makes it possible to design compounds with high specificity, as well as, compounds with multiple protein targets.
  • Ease of use geared towards medicinal chemists: allows easy monitoring of processes (from de novo design to calculation results) through a graphical user interface (GUI). The use of originally conceived structures is also allowed through a feature that enables the user to draw chemical structures via simple mouse operations.
The analysis window displayed above shows the result of a completed job in CzeekD. The left panel displays a plot showing scores and weight for each compound. Selecting a part of the plot enables display of detailed information with regards to compounds' various properties.

CzeekD is Readily available through the use of a web browser in a networked environment, as a cloud-based computational service. Kode is an official redistributor for CzeekS, please contact us for information on licensing and pricing of this software. Please visit the product’s page on Kyoto Constella website for further details.

Software type
On-line cloud service
No client-side installation is required, the service is accessed through normal web browsers (Firefox, Internet Explorer, Safari). Java (version 6 or above) and Adobe Flash Player (version 11 and above) are required.
How to get it
Contact us for information on licensing and pricing of this software.

This software is redistributed by Kode on behalf of Kyoto Constella Technologies.