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.

eCAMI – Simultaneous Classification and Motif Identification for enzyme/CAZyme annotation

eCAMI

:: DESCRIPTION

eCAMI is a Python package: (i) has the best performance in terms of accuracy and memory use for CAZyme and enzyme EC classification and annotation; (ii) the k-mer-based tools (including PPR-Hotpep, CUPP and eCAMI) perform better than homology-based tools and deep-learning tools in enzyme EC prediction.

::DEVELOPER

YIN LAB @ UNL & ZHANG LAB @ NKU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

eCAMI

:: MORE INFORMATION

Citation

Xu J, Zhang H, Zheng J, Dovoedo P, Yin Y.
eCAMI: simultaneous classification and motif identification for enzyme annotation.
Bioinformatics. 2020 Apr 1;36(7):2068-2075. doi: 10.1093/bioinformatics/btz908. PMID: 31794006.

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

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

:: 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.

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

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Chromatin Cutter

:: MORE INFORMATION

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.

CRHunter – Integrating multifaceted information to predict Catalytic Residues in Enzymes

CRHunter

:: DESCRIPTION

CRHunter is an integrative algorithm simultaneously use the complementarity between feature- and template-based methodologies and that between structural and sequence information.

::DEVELOPER

Rong Liu’s Lab of Protein Bioinformatics at Huazhong Agriculture University!

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web Browser
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Sci Rep, 6, 34044 2016 Sep 26
CRHunter: Integrating Multifaceted Information to Predict Catalytic Residues in Enzymes
Jun Sun , Jia Wang , Dan Xiong , Jian Hu , Rong Liu

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

Exit mobile version