Databases for Protein Sequences

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Databases for Protein Sequences
InterPro - Integrated Resource of Protein
Families, Domains and Sites

http//www.ebi.ac.uk/interpro/
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http//www.ebi.ac.uk/interpro/
InterPro Entry (accession) IPR000004
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(CONT.)
Results of Sequence Search Graphical Textual.
Smart
Pfam
ProDom
Prints
Prosite pattern
http//www.ebi.acuk/interpro/scan.html
Prosite profile
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InterPro Graphical View
Etc
Smart
Pfam
ProDom
Prints
Prosite pattern
Prosite profile
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http//smart.embl-heidelberg.de/
SMART (a Simple Modular Architecture Research
Tool) allows the identification of domains and
the analysis of domain architectures. Results
Other features and domains
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(CONT.)
PDBsum
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• Lecture 9
• Protein structure viewing
• PDB database, pdbsum, QuickPDB.
• NCBI MMDB (Molecular Modeling DataBase), Cn3D.
• 2. Protein Classification SCOP and CATH
  databases.
• 3. Families, Patterns, Motifs - InterPro.
• Databases prosite.
• Blocks.
• Pfam.
• eMOTIF.
• Other interesting protein features.
• 5. Other Diseases Related to Protein Folding.

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http//cubic.bioc.columbia.edu/mis/talks/course-20
01/cu2/sld085.htm
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Protein Cellular Location - PSORT
PSORT - prediction of protein localization sites
in cells.
http//psort.nibb.ac.jp/form.html
Result for GBA Amino acid composition tendency
for lysosomal protein.
PSORT Users' Manual http//psort.nibb.ac.jp/helpw
ww.htmlmtop
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Signal Peptide
http//www.nobel.se/medicine/laureates/1999/press.
html
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http//www.cbs.dtu.dk/services/SignalP/submission

INPUT
Note Submit only the N-terminal part of your
human amino acid sequence, not more than 50-70
amino acids. Organism group EUK Graphics
Include postscript graphics.
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SignalP Prediction - Output
scoring
pos aa C S Y
PostScript Graphics
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Protein Molecular Weight Prediction
http//www.ualberta.ca/stothard/javascript/prot
mw.html
Result The Protein Sequence Molecular Weight.
Output Results for 536 residue sequence starting
"MEFSSPSREE". The protein weighs 59.73
kilodaltons.
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Phosphorylation Sites
S T Y
Threshold
http//www.cbs.dtu.dk/services/NetPhos/
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E-mail results
Glycosylation sites prediction
Phosphorylation sites prediction
Etc.
http//www.EMBL-Heidelberg.DE/predictprotein/
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• Lecture 9
• Protein structure viewing
• PDB database, pdbsum, QuickPDB.
• NCBI MMDB (Molecular Modeling DataBase), Cn3D.
• 2. Protein Classification SCOP and CATH
  databases.
• 3. Families, Patterns, Motifs - InterPro.
• Databases prosite.
• Blocks.
• Pfam.
• eMOTIF.
• Other interesting protein features.
• 5. Other Diseases Related to Protein Folding.

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Alzheimer Disease

• Among the most common neurological diseases.
• The b-amyloid protein is 40 residues long and
• is cleaved from a larger precursor protein.
• When the precursor protein is mutated,
• ??????b-amyloid protein levels in the brain
  increase,
• leading to aggregation of the proteins.

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Prion Diseases
Mad Cow Disease (bovine spongiform
encephalopathy), Scrapie in sheep human
Creutzfeld Jacob disease

• The prion protein is present in normal brain
  tissues, where it
• apparently has a mostly alpha-helix
  conformation.
• In diseased brains, the same protein gain some
  beta-sheets
• and forms insoluble fibers that damage brain
  cells.
• The 1D sequence remains the same.
• The infectious nature of prion
• is believed to result from the
• ability of abnormal folded protein
• to catalyze the miss-folding
• of normal proteins.

Normal folding of prion protein
Abnormal folding of prion protein