Laboratory of Beneficial Microbes (Probiotics) for Crops and Sustainable Agriculture Kits (SAKs) for Subsistence Farmers
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   Protein, Enzyme and Proteomics Links

ExPASy Expert Protein Analysis System Links: protein structure prediction, threading, making phylogenetic trees, finding protein targeting sequences, finding post-translational modification sequences:
http://www.expasy.org/

UniProt Database, the world’ s largest catalog of proteins:
http://www.pir.uniprot.org/

Introduction to Enzymes
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/E/Enzymes.html

IUBMB Enzyme Nomenclature Database (for E.C. numbers)
http://www.chem.qmul.ac.uk/iubmb/enzyme/search.html

Enzyme Classification (E.C.) Tutorials
http://www.chem.qmul.ac.uk/iubmb/enzyme/

Review of Primary, Secondary, Tertiary Protein Structure:
http://bmbiris.bmb.uga.edu/wampler/tutorial/prot0.html
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/P/PrimaryStructure.html

Nice article on the importance of correct protein folding:
http://www.nature.com/horizon/proteinfolding/background/importance.html

Protein Databank (PDB) Database of 3D protein structures:
http://www.rcsb.org/pdb/Welcome.do

SCOP (Structural Classification of Proteins)
http://scop.berkeley.edu/intro.html

ProteinExplorer: free software to view proteins in 3D
http://www.umass.edu/microbio/chime/pe/protexpl/frntdoor.htm

STRAP – Structure Alignment Program for Proteins (free download)
For viewing aligned sequences on 3D protein structure
http://www.charite.de/bioinf/strap/

Introduction to Protein Folding
http://alpha2.bmc.uu.se/~lars/biowww/Proteinfolds.html

TargetP – Organelle targeting prediction
http://www.cbs.dtu.dk/services/TargetP/

ChloroP – Chloroplast targeting prediction
http://www.cbs.dtu.dk/services/ChloroP/

iGAP: Proteome 3D protein structure and domain assignment.
Genome Biol. (2003): 4, R51 (July 28)

MIPS: Analysis and annotation of protein - contains software.
Nucl. Acids. Res. (2004) Jan 1: 32
http://mips.gsf.de

AMPDB: Arabidopsis Mitochondrial Protein Database
Nucl. Acids. Res. (2005) 1, 33 D605-10
http://www.ampdb.bcs.uwa.edu.au/

PlantsP: Plant protein phosphorylation database:
Plant Cell (2004) 16, 2394-405.
http://plantsp.sdsc.edu

Organelle DB: A database to proteins localized to organelles and subcellular
Structures in diverse Eukaryotes (25,000 proteins, 60 organelles or structures)
Nucl. Acids. Res. (2005) 1, 33 D598-604 (Database Issue)
http://organelledb.lsi.umich.edu

AtNoPDB: Arabidopsis nucleolar protein database.
Nucl Acid Res.(2005) 1, D633-6
http://bioinf.scri.sari.ac.uk/cgi-bin/atnopdb/home

PHYTOPROT: Clustering of plant proteins in families.
Nucl. Acid. Res. (2004): 32: D351-3.

 

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