Pajek Writer – Generation of Structural Representation of Biochemical Processes in Format Pajek

Pajek Writer

:: 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

Biomodels Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • Java

:: DOWNLOAD

 Pajek Writer

:: MORE INFORMATION

DynaFit 4.06.007 – Enzyme Kinetic Data Analysis

DynaFit 4.06.007

:: 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

BioKin, Ltd.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

DynaFit

:: 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”

ENZO – Building Kinetic Models of Enzyme Catalyzed Reactions

ENZO

:: DESCRIPTION

ENZO (Enzyme Kinetics) is a web tool for easy construction and quick testing of kinetic models of enzyme catalyzed reactions.

::DEVELOPER

ENZO team

:: SCREENSHOTS

ENZO

:: REQUIREMENTS

  • Web browser

:: 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.

Scaffold Hunter 2.6.3 – Analysis of Structure-related Biochemical data

Scaffold Hunter 2.6.3

:: 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

Scaffold Hunter team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux/  MacOSX
  • Java

:: DOWNLOAD

Scaffold Hunter

:: 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.

BioSM 1.00 – Identify Biochemical Structures in Chemical Structure Space

BioSM 1.00

:: 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

  • Windows / Linux/ MacOsX
  • Java

:: DOWNLOAD

BioSM

:: 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.

MACiE 3.0 – Exploring the Diversity of Biochemical Reactions

MACiE 3.0

:: DESCRIPTION

MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of fully annotated enzyme reaction mechanisms.

::DEVELOPER

Thornton group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: 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.

Biochemistry Lab Suite 3.0.1 – Tools Covering different fields of Biochemistry, Biology and Chemistry

Biochemistry Lab Suite 3.0.1

:: 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

rpor

:: SCREENSHOTS

BiochemistryLS

:: REQUIREMENTS

  • Android

:: DOWNLOAD

 Biochemistry Lab Suite 

:: MORE INFORMATION

BISEN 1.0.6 – Biochemical Simulation Environment

BISEN 1.0.6

:: 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

  • Windows / Linux / MacOsX
  • MatLab

:: DOWNLOAD

 BISEN

:: 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.

ECOH 0.91.4 – Enzyme COmmission numbers Handler

ECOH 0.91.4

:: 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

ECOH

::REQUIREMENTS

  • Linux/ MacOsX/Windows
  • Java

:: DOWNLOAD

 ECOH

:: 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.

Prometheus 0.8.0 – Storage, Management, and Analysis of Fermentation data

Prometheus 0.8.0

:: 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

  • Linux / Windows / MacOsX
  • Java
  • Oracle / PostgreSQL / MySQL

:: DOWNLOAD

 Prometheus

:: 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