:: DESCRIPTION
Pajek Writer – software for generation of structural representation of biochemical processes in format Pajek on a set of the proceeding reactions presented in the form of the list of biochemical reactions.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
DynaFit – analysis of (bio)chemical kinetics and equilibria.
The main purpose of the program DynaFit is to perform nonlinear least-squares regression of chemical kinetic, enzyme kinetic, or ligand-receptor binding data. The experimental data can be either initial reaction velocities in dependence on the concentration of varied species (e.g., inhibitor concentration vs. velocity), or the reaction progress curves (e.g., time vs. absorbance).
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Request Free DynaFit Academic License
If you publish any results obtained by using DYNAFIT, plase cite the following reference:
Kuzmic, P. (1996) Anal. Biochem. 237, 260-273.
“Program DYNAFIT for the Analysis of Enzyme Kinetic Data: Application to HIV Proteinase”
:: DESCRIPTION
ENZO (Enzyme Kinetics) is a web tool for easy construction and quick testing of kinetic models of enzyme catalyzed reactions.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
PLoS One. 2011;6(7):e22265. doi: 10.1371/journal.pone.0022265. Epub 2011 Jul 19.
ENZO: a web tool for derivation and evaluation of kinetic models of enzyme catalyzed reactions.
Bevc S1, Konc J, Stojan J, Hodošček M, Penca M, Praprotnik M, Janežič D.
:: DESCRIPTION
Scaffold Hunter is a tool for the visual analysis of data from the life sciences, aiming at intuitive access to large and complex data sets that offers a variety of views and analysis methods. It originates from drug discovery and has evolved into a reusable open source platform for a wider range of applications.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Scaffold Hunter: a comprehensive visual analytics framework for drug discovery.
Schäfer T, Kriege N, Humbeck L, Klein K, Koch O, Mutzel P.
J Cheminform. 2017 May 11;9(1):28. doi: 10.1186/s13321-017-0213-3.
:: DESCRIPTION
BioSM is a cheminformatics tool that uses known mammalian biochemical compounds (scaffolds) and graph matching methods to identify biochemical structures in chemical structure space
::DEVELOPER
Bioinformatics Lab , Computer Science & Engineering Dept. University of Connecticut
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
J Chem Inf Model. 2013 Mar 25;53(3):601-12. doi: 10.1021/ci300512q. Epub 2013 Feb 27.
BioSM: metabolomics tool for identifying endogenous mammalian biochemical structures in chemical structure space.
Hamdalla MA1, Mandoiu II, Hill DW, Rajasekaran S, Grant DF.
:: DESCRIPTION
MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of fully annotated enzyme reaction mechanisms.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
MACiE: exploring the diversity of biochemical reactions.
Holliday GL, Andreini C, Fischer JD, Rahman SA, Almonacid DE, Williams ST, Pearson WR.
Nucleic Acids Res. 2012 Jan;40(Database issue):D783-9.
:: DESCRIPTION
Biochemistry Lab Suite app aims in helping scientists and students working in the field of mass spectrometry based proteomics, metabolomics, biochemistry, biology and chemistry but also aids in general lab work.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
The BISEN software package is a suite of tools for generating equations and associated computer programs for simulating biochemical systems
::DEVELOPER
The Virtual Physiological Rat Project
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2009 Mar 15;25(6):836-7. doi: 10.1093/bioinformatics/btp069. Epub 2009 Feb 25.
BISEN: Biochemical Simulation Environment.
Vanlier J, Wu F, Qi F, Vinnakota KC, Han Y, Dash RK, Yang F, Beard DA.
:: DESCRIPTION
ECOH is a new method to assign Enzyme Commission numbers using a maximum common substructure algorithm, mutual information and a support vector machine.
::DEVELOPER
Department of Bioinfomatics, Ritsumeikan Univ.
:: SCREENSHOTS
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2013 Feb 1;29(3):365-72. doi: 10.1093/bioinformatics/bts700. Epub 2012 Dec 5.
ECOH: An Enzyme Commission number predictor using mutual information and a support vector machine.
Matsuta Y, Ito M, Tohsato Y.
:: DESCRIPTION
Prometheus is a versatile software platform for the storage, management, and analysis of fermentation data. The multi application system allows storing of arbitrary online and offline parameters and supports gene expression studies by including existing applications for microarray and qPCR analysis. The newly developed application Prometheus features data import, runtime chart generation, data statistics, and a versatile data export mechanism. The platform can be accessed using a web browser and exposes many functions as a web service. The complete system is protected by a user management system providing single sign on and fine grained data sharing mechanisms.
::DEVELOPER
Genomics & Bioinformatics Graz, Graz University of Technology
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Rader R, Pabinger S, Specht T, Ramsauer T, Trajanoski Z.
Prometheus: Integrating bioprocess and gene expression data for industrial bioprocess optimization.
submitted