TINKER – Design Metabolic Paths using the Known Universe of Enzymes and Reactions

TINKER

:: DESCRIPTION

TINKER is a metabolic pathway design/search tool. It compiles the entire set of known reactions and compounds from the latest version of the Rhea database and converts this data into a directed graph

::DEVELOPER

OSS-Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java

:: DOWNLOAD

 TINKER

:: MORE INFORMATION

Citation

Metabolic tinker: an online tool for guiding the design of synthetic metabolic pathways.
McClymont K, Soyer OS.
Nucleic Acids Res. 2013 Jun;41(11):e113. doi: 10.1093/nar/gkt234.

PRIAM 201303 – Sequence Profiles Generated from the ENZYME database

PRIAM 201303

:: DESCRIPTION

PRIAM (PRofils pour l’Identification Automatique du Métabolisme) is a method for automated enzyme detection in a fully sequenced genome, based on all sequences available in the ENZYME database.PRIAM relies on sets of position-specific score matrices (PSSMs) automatically tailored for each ENZYME entry. The whole Swiss-Prot database has been used to parameterise and to assess the method. As an example, PRIAM was applied to predict metabolic pathways from the complete genome of the nitrogen fixing bacterium Sinorhizobium meliloti and on the plant pathogen Ralstonia solanacearum. The results of this automated annotation method were compared with the original genome annotation and visualised on KEGG graphs in order to facilitate the interpretation of predicted metabolic pathways and to highlight potentially missing enzymes.

::DEVELOPER

PRIAM Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX/ Windows
  • Java

:: DOWNLOAD

 PRIAM 

:: MORE INFORMATION

Citation

Clotilde Claudel-Renard, Claude Chevalet, Thomas Faraut and Daniel Kahn
Enzyme-specific profiles for genome annotation: PRIAM
Nucleic Acids Research, 2003, Vol. 31, No. 22 6633-6639

PHYPred – Identifying Phage Enzymes and Hydrolases

PHYPred

:: DESCRIPTION

The web-server PHYPred was developed to identify the phage enzymes and hydrolases based on the sequence information.

::DEVELOPER

LinDing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PHYPred: a tool for identifying bacteriophage enzymes and hydrolases.
Ding H, Yang W, Tang H, Feng PM, Huang J, Chen W, Lin H.
Virol Sin. 2016 Aug;31(4):350-2. doi: 10.1007/s12250-016-3740-6.

EC-BLAST – A Novel Tool to Map Reactions and Compare Enzymes

EC-BLAST

:: DESCRIPTION

EC-BLAST is an algorithm and Web tool for quantitative similarity searches between enzyme reactions at three levels: bond change, reaction center and reaction structure similarity.

::DEVELOPER

Thornton group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

EC-BLAST: a tool to automatically search and compare enzyme reactions.
Rahman SA, Cuesta SM, Furnham N, Holliday GL, Thornton JM.
Nat Methods. 2014 Feb;11(2):171-4. doi: 10.1038/nmeth.2803.

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.

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”

Enzymatic! 1.0 – Enzyme Learning Game

Enzymatic! 1.0

:: DESCRIPTION

Enzymatic! is an enzyme learning game.ENZYMES are extremely important in Biology! Essentially EVERY life process relies for EVERY living thing relies on ENZYMES! So… it might be important to understand them (at least a little bit…) In this amazing interactive experience, you will learn about enzymes by playing games, performing virtual experiments, and solving puzzles!

::DEVELOPER

BioMan Biology

:: SCREENSHOTS

Enzymatic

:: REQUIREMENTS

  • Web browser / iPad/ iPhone

:: DOWNLOAD

 Enzymatic!

:: MORE INFORMATION

Chromatin Cutter 1.00 – Simulates the distribution of DNA in a Gel Electrophoresis Study of Yeast Chromatin cut by Enzymes

Chromatin Cutter 1.00

:: DESCRIPTION

Chromatin Cutter simulates the distribution of DNA in a gel electrophoresis study of Yeast chromatin cut by enzymes. It lets you specify the fraction of nucleosomes that are unwrapped (wrapped ones have inaccessible DNA). It lets you specify the variance in the distribution of nucleosomes around their mean distance. It lets you specify the number of cuts per unit length (enzyme concentration). It plots the effects of these on the log number of base pairs, which matches the gel electrophoresis mass distribution.

::DEVELOPER

CISMM (Computer Integrated Systems for Microscopy and Manipulation)

:: SCREENSHOTS

ChromatinCutter

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Chromatin Cutter

:: MORE INFORMATION

L1pred – Prediction tool for Catalytic Residues in Enzymes

L1pred

:: DESCRIPTION

L1pred is a sequence-based prediction tool for catalytic residues in enzymes with the L1-logreg classifier

::DEVELOPER

System Biology Laboratory Of Chi Zhang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 L1pred

 :: MORE INFORMATION

Citation

PLoS One. 2012;7(4):e35666. doi: 10.1371/journal.pone.0035666. Epub 2012 Apr 27.
L1pred: a sequence-based prediction tool for catalytic residues in enzymes with the L1-logreg classifier.
Dou Y1, Wang J, Yang J, Zhang C.

EzyPred – Predicting Enzyme Functional Classes and Sub-classes

EzyPred

:: DESCRIPTION

EzyPred is a top-down approach for predicting enzyme functional classes and sub-classes purely based on protein sequences.

::DEVELOPER

Computational Systems Biology Group, Shanghai Jiao Tong University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

EzyPred: a top-down approach for predicting enzyme functional classes and subclasses.
Shen HB, Chou KC.
Biochem Biophys Res Commun. 2007 Dec 7;364(1):53-9.