Modeling Biomolecules Using the WWW

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Modeling Biomolecules Using the WWW
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Major Classes of Biomolecules

• Peptides (Proteins)
• Carbohydrates
• Nucleic Acids
• Lipids

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Modeling Peptides

• Primary structure
• Most molecular modeling software allows
  construction of peptide models by appending
  pre-constructed amino acids in sequence, usually
  by selecting their 1- or 3-letter abbreviations.
• Secondary structure
• features such as a-helix, b (pleated) sheet,
  hairpin turns, etc. can be specified (examples on
  following panel).

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Alpha Helix Secondary Structure
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Beta Sheet Secondary Structure
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Hairpin Turn Secondary Structure
Hairpin turn, alpha helix
Hairpin turn, Beta sheet
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Modeling Peptides...

• Tertiary structure
• folding of chainsmore difficult to model
  accurately, unless structure is known from
  X-ray or NMR.
• Quaternary structure
• Combination of several subunits...likewise
  difficult to model accurately, unless structure
  is known from X-ray or NMR.

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Modeling Peptides...

• Computations are usually limited to molecular
  mechanics, although semi-empirical MO
  calculations can be performed on small
  biopolymers.
• MM Forcefields designed for biomolecules
• Amber (peptides and nucleic acids)/Kollman
• OPLS (peptides and nucleic acids)/Jorgensen
• BIO (biomacromolecules)/Karplus
• (all of these are found in HyperChem)

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Modeling Biomolecules using HyperChem
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HyperChem

• Special database for Peptides
• 20 Pre-optimized amino acids
• Peptide menu choices
• a helix
• b (pleated) sheet
• other
• Termination modes
• NH2 or NH3 CO2H or CO2-

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Spartan

• Special database for Nucleotides
• 4 Pre-optimized bases (A,T,C,G)
• Nucleotide menu choices
• DNA (double strand), DNA (single strand)
• RNA (double strand), RNA (single strand)
• DNA-RNA mixed
• A, B or Z helical forms (differ in rise/base)

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WWW pages dealing with Modeling Biomolecules

• Georgia State University molecular modeling site
  modeling problems, biomolecules
  http//heme.gsu.edu/glactone/
• Dr. Barry Honigs web site (Columbia University
  great images of biomolecules)http//wiki.c2b2.
  columbia.edu/honiglab_public/index.php/Main_Page

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WWW pages dealing with Modeling Biomolecules...

• Molecular Graphics (rendering) University of
  Geneva, Switzerland (Dr. Jacques Weber)
• http//scsg9.unige.ch/fln/eng/toc.html
• NIH Center for Molecular Modeling http//cmm.info.
  nih.gov/modeling/

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WWW pages dealing with Modeling Biomolecules...

• Molecular Modeling Research Group at the Dept. of
  Agricultural Environmental Sciences and Food
  Biotechnology, University of Sassari -
  ITALYhttp//antas.agraria.uniss.it
• The Research Collaboratory for Structural
  Bioinformatics (PDB database of structures of
  proteins and other biomolecules)http//www.rcsb.
  org