Protein structure prediction by rBZ8GsU3

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									    Protein structure prediction
Anttu Kurttio
Ville Pietiläinen
              Introduction
• Proteins are one of the most important
  parts in any biological systems.
• Understanding the folding of the amino-
  acid chain to produce functional proteins is
  essential for studying cellular systems.
• Fast and accessible methods of solving
  the 3D structure of a protein are in high
  demand.
          Protein structure
• This topic has been covered several times.
  Next! 
     Computational methods
• Ab initio- methods
  – Laws of physics + amino-acid sequence =
    protein structure
  – Computes potential energy functions.
  – Minimum potential energy is the most stable
    structure and as such the most likely.
  – Computationally demanding.
       Comparative methods
• Based on the limited amount of possible
  tertiary structure types.
• Approximately 2000 different types of
  protein folds.
• Comparing the sample to a database of
  known structures, for example Protein
  Data Bank.
        Homology modelling
• Based on the assumption that homologous
  (related) proteins fold in a similar fashion.
• Folding is a highly conserved factor, much
  more so than amino-acid sequence.
• Finding a match between two distantly
  related proteins can be difficult.
          Protein threading
• Based on the assumption that similar
  folding has already been found.
• Comparing parts of the sequence to a
  database of known three dimensional
  structures using a scoring function.
• Works at least somewhat on
  approximately 80% of new protein
  sequences.
              Programs
• A lot of free programs are available.
• Server based programs do the
  computational work. For example Swiss-
  Model, Rosetta or PSIPRED.
• Downloadable applications are used for
  viewing the results. For example Swiss-
  PdbViewer or Rasmol.
• Distributed computing promises increases
  in computational capacity.
                        DEMO
• Swiss-Model in four easy steps.




swissmodel.expasy.org
Step 1: Send in the sequence
Step 2: Coffee break
Step 3: Recieve mail
Step 4: Open PDB-file
                Rejoice!
• Study your brand new model of a protein.




              

								
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