PPS '97Syllabus
Course Index
Syllabus Index
Term 1
Term 2
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Overview of Molecular
Forces
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Preliminary considerations -
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Interactions, forces and energies
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Electromagnetic interactions dominate on the molecular scale
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The Born-Oppenheimer approximation
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Quantum chemistry can (theoretically) deal with all molecular interactions
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Advanced topic: A brief introduction to quantum chemistry.
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Advanced topic: The application of quantum chemistry to protein simulation.
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Covalent Interactions
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Simplified models of interaction
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Covalent Bonds
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Bond Angles
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Dihedral Angles
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Non-bonded Interactions
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Electrostatic interactions
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Induction and Dispersion
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Repulsion terms
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Hydrogen bonding
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The effect of solvent and hydrophobic interactions
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Dielectric effects
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The hydrophobic effect
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Advanced topic: The hydrophobic effect and protein unfolding
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Potential energy functions and simulation methods
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Potential energy functions
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Energy minimization
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Molecular Dynamics
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Other simulation methods
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Secondary Structure
In Detail
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Background and History
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Introduction to Terminology
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Types of Secondary Structure
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Helices
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Sheets
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Antiparallel
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Parallel
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Twists
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Bulges
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Strand connections
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Turns
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gamma
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I, I'
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II, II'
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III, III'
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Other
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Identification of Secondary Structure
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Identification in 3D Structures
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Identification without 3D Structure
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Prediction of Secondary Structure
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homology
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statistical
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stereochemical
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Tertiary Structure,
Part I
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Tertiary Structure, Part II
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Domains
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Domain Folds
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All-Alpha
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The Lone Helix
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Helix-turn-helix
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The Four-helix Bundle
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DNA-binding domains
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Globins
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All-Beta
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Up-and-down Antiparallel Beta Sheets
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Greek Key
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Jellyroll
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Beta Propellors
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Beta Trefoils
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Beta Helix
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Alpha/Beta
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Rossman Fold
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alpha/beta horseshoe
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alpha/beta barrels
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singly wound
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doubly wound; variations
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Alpha+Beta
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Small disulphide rich proteins
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Types of proteins
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Introduction
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Globular (Water-Soluble) Proteins
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Membrane Proteins
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Fibrous and Structural Proteins
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Mosaic Proteins
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Protein Structure Databases
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Quaternary Structure
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Introduction
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Symmetry
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Enzyme & Other Multimers
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Multi-Enzyme Complexes
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Larger Assemblies and Aggregations
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Protein Interactions
overview
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Binding
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inhibitor proteins
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messaging; Signal Transduction Pathways
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adhesion
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Enzymes
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Enzyme nomenclature databases
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ENZYME
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UCL Enzyme Structures Database
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Lysis
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proteolysis: the 4 families of proteases
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of polysaccharides
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of Lipids
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Conformational changes
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allostery: haemoglobin
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larger scale movements: muscle fibres
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Protein Motions database
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