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CAZy

http://www.cazy.org/

Description :
Carbohydrate-Active Enzymes database

FCP

http://cgl.imim.es/fcp/

Description :
Tools and resources for translating the remarkable growth witnessed in recent years in the number of protein structures determined experimentally into actual gain in the functional coverage of the proteome are becoming increasingly necessary. We introduce FCP, a publicly accessible web tool dedicated to analyzing the current state and trends of the population of structures within protein families. FCP offers both graphical and quantitative data on the degree of functional coverage of enzymes and nuclear receptors by existing structures, as well as on the bias observed in the distribution of structures along their respective functional classification schemes.

References :
1. R. García-Serna, L. Opatowski, J. Mestres. (2006) FCP: Functional Coverage of the Proteome by Structures. Bioinformatics 22: 1792-1793

ExplorEnz

http://www.enzyme-database.org/

Description :
Reference database of the IUBMB Enzyme Nomenclature

PRECISE

http://precise.bu.edu/precisedb/

Description :
Predicted and consensus interaction sites in enzymes

PROCOGNATE

http://www.ebi.ac.uk/thornton-srv/databases/procognate/index.html

Description :
Protein cognate ligands for the domains in enzyme structures

MetaCrop

http://metacrop.ipk-gatersleben.de/

Description :
Biochemical pathways and enzymes in crop plants

3D-Fun

http://3dfun.bioinfo.pl/

Description :
3D-Fun is software for predicting enzyme function from structure rather than sequence. Users input protein coordinates in PDB format to which all known protein structures are compared by 3D structural superposition. Superposition results are displayed through interactive graphics.

E1DS

http://e1ds.ee.ncku.edu.tw/

Description :
E1DS is a web server for enzyme catalytic site prediction. Annotation of enzymes is made using a novel pattern mining algorithm that discovers long sequence motifs.

DyNAVacS

http://202.54.26.221/dynavac/

Description :
DyNAVacS is a tool for designing DNA vaccines that includes steps for chosing a suitable expression vector, ensuring optimal expression by codon optimization, engineering CpG motifs for enhancing immune responses, and providing additional sequence signals for efficient translation. It also allows includes restriction enzyme mapping and design of primers spanning user specified sequences.

NEBcutter

http://tools.neb.com/NEBcutter/index.php3

Description :
NEBcutter finds non-overlapping open reading frames and sites for all enzymes that cut the sequence just once; max length is 100 kb.

REBASE

http://rebase.neb.com/rebase/rebase.html

Description :
The Restriction Enzyme Database, a collection of information about restriction enzymes and related proteins.

REPK

http://rocaplab.ocean.washington.edu/tools/repk

Description :
REPK (Restriction Endonuclease Picker) assists in the choice of restriction endonucleases for terminal restriction fragment length polymorphism (T-RFLP) by finding sets of four restriction endonucleases which together uniquely differentiate user-designated sequence groups.

Software for MacOSX at Mek&Tosj.com

http://www.mekentosj.com/programs/index.html

Description :
Freely available programs that run on the MacOSX platform. 4Peaks is a DNA sequence editor and visualization program able to read and write common trace file formats. iRNAi assists in the design of error-free oligos. EnzymeX is a tool to help determine which restriction enzymes to use and includes information for over 580 enzymes. LabAssistant is a task/time management system to help organize your experiments.

WatCut

http://watcut.uwaterloo.ca/watcut/template.php

Description :
WatCut allows you to perform restriction analysis and silent mutation analysis. The restriction analysis results can be displayed as a table or graphically to compare the results of different digests. All commercially available type II restriction enzymes are known. The silent mutation analysis scans your oligonucleotide sequence for restriction sites that could be introduced without altering the protein that is encoded.

BRENDA - The Comprehensive Enzyme Information System

http://www.brenda.uni-koeln.de/

Description :
Information about reaction and specificity, post-translational modifications, structure, stability, and references to other databases; free for academics.

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