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Modeling Biomolecules Using the WWW. Major Classes of Biomolecules. Peptides (Proteins) Carbohydrates Nucleic Acids Lipids. Modeling Peptides. Primary structure

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Modeling Biomolecules Using the WWW

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Modeling Biomolecules Using the WWW

Major Classes of Biomolecules

  • Peptides (Proteins)

  • Carbohydrates

  • Nucleic Acids

  • Lipids

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).

Alpha Helix Secondary Structure

Beta Sheet Secondary Structure

Hairpin Turn Secondary Structure

Hairpin turn, alpha helix

Hairpin turn, Beta sheet

Modeling Peptides...

  • Tertiary structure

    • folding of chains…more 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.

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)

Modeling Biomolecules using 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-


  • 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)

WWW pages dealing with Modeling Biomolecules

  • Georgia State University molecular modeling site: modeling problems, biomolecules:

  • Dr. Barry Honig’s web site (Columbia University… great images of biomolecules):

WWW pages dealing with Modeling Biomolecules...

  • Molecular Graphics (rendering); University of Geneva, Switzerland (Dr. Jacques Weber)

  • NIH Center for Molecular Modeling

WWW pages dealing with Modeling Biomolecules...

  • Molecular Modeling Research Group at the Dept. of Agricultural Environmental Sciences and Food Biotechnology, University of Sassari - ITALY:

  • The Research Collaboratory for Structural Bioinformatics (PDB database of structures of proteins and other biomolecules):

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