Molecular viewers and protein structure prediction
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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 l.jpg
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 l.jpg
Protein structure viewers

  • RasMol

  • Deep View

  • Cn3D

  • WebLabViewer

  • PyMol

  • Chimera


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Steps to tertiary structure prediction

  • Comparative protein modeling

    • Extrapolates new structure based on related family members

  • Steps

    • Identification of modeling templates

    • Alignment

    • Model building


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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


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Alignment

  • “Common core” and conserved loops of target sequence are threaded onto the template structure using only alpha carbons



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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.


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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


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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


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