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

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  • Modeling Biomolecules Using the WWW

  • Major Classes of BiomoleculesPeptides (Proteins)CarbohydratesNucleic AcidsLipids

  • Modeling PeptidesPrimary structureMost 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 structurefeatures 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 StructureHairpin turn, Beta sheetHairpin turn, alpha helix

  • Modeling Peptides...Tertiary structurefolding of chainsmore difficult to model accurately, unless structure is known from X-ray or NMR.Quaternary structureCombination 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)/KollmanOPLS (peptides and nucleic acids)/JorgensenBIO+ (biomacromolecules)/Karplus(all of these are found in HyperChem)

  • Modeling Biomolecules using HyperChem

  • HyperChemSpecial database for Peptides20 Pre-optimized amino acids Peptide menu choices a helix b (pleated) sheet otherTermination modes: NH2 or NH3+; CO2H or CO2-

  • SpartanSpecial database for Nucleotides4 Pre-optimized bases (A,T,C,G)Nucleotide menu choicesDNA (double strand), DNA (single strand)RNA (double strand), RNA (single strand)DNA-RNA mixedA, 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 Honigs 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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