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.

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.

BioSMXpress – Identification of unknown Biochemical Structures in Metabolomics

BioSMXpress

:: DESCRIPTION

BioSMXpress was designed and developed as an enhancement to BioSM. BioSMXpress is, on average, 8 times faster than BioSM without compromising the quality of the predictions made. BioSMXpress will be an extremely useful tool in the timely identification of unknown biochemical structures in metabolomics.

::DEVELOPER

Mai Hamdalla , Sanguthevar Rajasekaran

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • JRE

:: DOWNLOAD

 BioSMXpress

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2015 Mar 18;16 Suppl 5:S11. doi: 10.1186/1471-2105-16-S5-S11.
A molecular structure matching approach to efficient identification of endogenous mammalian biochemical structures.
Hamdalla MA, Ammar RA, Rajasekaran S.

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”

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

Group of Molecular Genetic Systems Modeling

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • Java

:: DOWNLOAD

 Pajek Writer

:: MORE INFORMATION

FermentVelocity – Generation of Enzymatic Reaction Velocity Equations

FermentVelocity

:: DESCRIPTION

FermentVelocity – the program for generation of the enzymatic reaction velocity equations on basis of the reaction’s mechanism. The generation process is based on the King-Altman algorithm.

::DEVELOPER

Group of Molecular Genetic Systems Modeling

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Windows

:: DOWNLOAD

 FermentVelocity

:: MORE INFORMATION

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.