Lecture 9: Structure Viewing,

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Lecture 9 Structure Viewing, Families, Motifs
Domains
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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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Secondary Structure Prediction Software
PHD sec
Secondary structure prediction based on analysis
based on PSI-BLAST.
Based on threading.
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Three Main Approaches for Structural Prediction
1. Comparative (Homology) Modeling. 2. Fold
Recognition (Threading). 3. Ab-Initio (based
only on sequence). Principles Look for the
structure with minimum free energy. The main
driving force for folding is to pack hydrophobic
side-chains into the interior of the molecule,
thus creating a hydrophobic core. Factors
other than free energy shape, size, polarity,
strength of interactions, etc.
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Predicting vs Viewing
There are many programs for visualizing the 3D
structures of proteins. They typically offer
different viewpoints, each revealing a
different aspect of the 3D structure.
Rasmol, CN3D
While doing a great visualization job, these
programs have nothing to do with predicting the
structure.
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A Tour of Protein Structure Databases and
Visualization Tools
Secondary structure
Tertiary structure

• Rasmol - Most commonly used viewer, uses PDB
  format.
• CN3D - Provides viewing of 3D structures from
  Entrez,
• uses MMDB format.

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PDB - DataBank of Protein Structures
http//www.rcsb.org/pdb/ (PDB code - 1E4I
glucosidase).
For understanding important features of PDB, look
at the animated presentation http//www.rcsb.org/
images/ashtons.swf
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Ligands
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3D structures of beta-glucosidase.
Ribbons
Cylinders
http//www.rcsb.org/pdb/
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Page 1
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PDBSum - Page 2
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PDBSum - Page 3
(TOPS)
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Quick PDB
Features
Alpha helix, beta sheet, other (loops). Can
rotate. Click for a mutation and find where it
is. Special areas on the molecule.
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http//beta.rcsb.org/pdb/cgi/models.cgi
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NCBI's structure database MMDB (Molecular
Modeling DataBase)
http//www.ncbi.nlm.nih.gov/Structure/index.shtml
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ENTREZ
http//www.ncbi.nlm.nih.gov/Structure/MMDB/mmdb.sh
tml
View with Cn3D
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Structure Viewing Using Cn3D
N-terminus
C-terminus
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N-terminus
Structure Viewing Using Cn3D
C-terminus
Choose Go to Style, edit Global Style. Go to
Labels choose spacing every 20 amino
acids. Type 1 letter. Click Termini ON.
Sequence Window
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Structure Alignment
http//123d.ncifcrf.gov/run2.html
http//123d.ncifcrf.gov/Help.html
Saposin fold
taken from PDB
Surfactant
Link for results
Quick PDB