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Learn how to display and manipulate protein structures with Deep View. Workshop-Learn how to use Deep View molecular modeler. Protein structure viewers. RasMol ...

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molecular viewers and protein structure prediction
Molecular viewers and protein structure prediction
  • May 28, 2009
  • Quiz #3
  • Return HW #8
  • Learn how to obtain information about a protein from a motif search. Learn how to display and manipulate protein structures with Deep View.
  • Workshop-Learn how to use Deep View molecular modeler.
protein structure viewers
Protein structure viewers
  • RasMol
  • Deep View
  • Cn3D
  • WebLabViewer
  • PyMol
  • Chimera
steps to tertiary structure prediction
Steps to tertiary structure prediction
  • Comparative protein modeling
    • Extrapolates new structure based on related family members
  • Steps
    • Identification of modeling templates
    • Alignment
    • Model building
identification of modeling templates
Identification of modeling templates
  • One chooses a cutoff value from FastA or BLAST search (E <10-5)
  • Up to ten templates can be used but the one with the highest sequence similarity to the target sequence (lowest E-value) is the reference template
  • Ca atoms of the templates are selected for superimposition.
    • This generates a structurally corrected multiple sequence alignment
alignment
Alignment
  • “Common core” and conserved loops of target sequence are threaded onto the template structure using only alpha carbons
building the model
Building the model
  • Framework construction
    • Average the position of each atom in target, based on the corresponding atoms in template.
  • Portions of the target sequence that do not match the
  • template are constructed from a “spare part” algorithm.
  • Each loop is defined by its length and C atom
  • coordinates of the four amino acids preceding
  • and following the loop.
building the model8
Building the model
  • Completing the backbone-a library of PDB entries is consulted to add carbonyl groups and amino groups. The 3-D coordinates of the carbonyl groups and amino groups come from a separate library of pentapeptide backbone fragments. These backbone fragments are fitted onto the target C alpha carbons.
  • Side chains are added from a table of most probable rotamers corresponding to a particular backbone conformation.
  • Model refinement-minimization of energy
protein modeling workshop
Protein Modeling Workshop
  • Continue to work through the first 11 chapters of the tutorial you began in the previous class. (http://www.usm.maine.edu/~rhodes/SPVTut/text/SPdbVTut.html)
  • Perform the protein modeling exercise described at: http://us.expasy.org/spdbv/text/modeling.htm