CzeekS

CzeekS is powerful software tool, developed by Kyoto Constella Technologies, for high-speed screening of compound-protein interactions using Chemical Genomics-Based Virtual Screening (CGBVS). Thanks to the CGBVS technology, active compounds can be predicted from the binding patterns obtained from the interaction (chemogenomics data) of proteins (biological space) and compounds (chemical space). A scientific paper explaning the CGBVS, with a case study, is available (published as open access) for further details:

Yabuuchi et al. "Analysis of multiple compound-protein interactions reveals novel bioactive molecules." Molecular systems biology 7.1 (2011): 472.

CzeekS
The illustration above,indicates multiple interaction between compounds (in the chemical space) and target proteins (in the biological space). CGBVS, the core technology behind CzeekS, utilizes these interaction data to perform efficient screening of compounds.

CzeekS provides a wide list of models ready to be used, and the user can build new models, or refine the existing ones, using his/her own in-house assay data. The actually available models are the following:

Model Target proteins Interactions Details (Proteins and protein groups)
GPCR 242 158,405 Class Aα, Class Aβ, Class Aδ, Class Aγ, Class B, Class C
Kinase 412 154,079 AGC, CAMK, CMGC, STE, TK, TKL, others
Ion channel 218 142,282 Voltage-gated, Ligand-gated, others
Transporter 148 112,659 Electrochemical, ATPase, ATP-binding cassette, others
Nuclear receptor 41 139,051 NR1, NR2, NR3, NR4, NR5
Protease 229 141,691 Endopeptidase, Exopeptidase

A further set of models have been recently added, the ChEMBL models - based on data obtained from ChEMBL database (Release 21) and offered for free:

Model Target proteins Interactions Details (Proteins and protein groups)
GPCR 213 64,827 Class Aα, Class Aβ, Class Aδ, Class Aγ, Class B, Class C
Kinase 272 45,041 AGC, CAMK, CMGC, STE, TK, TKL, others
Ion channel 135 16,040 Voltage-gated, Ligand-gated, others
Transporter 80 8,491 Electrochemical, ATPase, ATP-binding cassette, others
Nuclear receptor 38 15,252 NR1, NR2, NR3, NR4, NR5
Protease 180 27,678 Endopeptidase, Exopeptidase

Some of CzeekS features:

  • Command line interface (cli): enables high speed and highly accurate in silico compound screening.
  • Multi-target screening: scoring against multiple protein targets can be done taking compound selectivity into account.
  • Search for the target protein of a particular compound: scoring against all the proteins present in a selected model can be implemented in a compound-by-compound basis, allowing the search for the target protein.
  • Creation of new or refinement of existing models through the addition of client's data: prediction models can be refined through the addition client's assay data. Prediction accuracy of the learning model is expected to increase by the addition of client's data.
  • Line-up of various prediction models: in addition to standard models (GPCR, Kinase, Ion channel, Transporter, Nuclear receptor, Protease), models focusing on subfamilies are also included. Models can be chosen according to the client's specific needs.
  • Multi-core CPUs support (OpenMP Parallelization): running CzeekS in systems with multi-core CPUs enables much faster CGBVS calculations.

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.

CzeekS

Software type
Standalone command-line application (with support for multi-core and cluster systems)

Requirements
RAM: at least 16 MB
Disk space: at least 100 GB
Operative Systems: Linux (CentOS, Fedora Core)

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.

Kyoto Constella Technologies