Protein Modeling in Education:
A protein experiment for teaching
e D. Purvis III
CAChe Group, Fujitsu
Beaverton, Oregon
Nigel Richards
University of Florida
Gainesville, Florida
Teaching with Laboratory exercises
Student Crispin Wong and Prof. James Currie
Pacific University
20 Experiments in General, Organic, Physical, anic
1 Calculating the Geometry of Molecules and Ions
2 ics of Substitution Reactions
3 Sunscreen and Ultraviolet Absorption
4 Conformations of Menthone and Isomenthone
5 The Evelyn Effect
6 Prediction of Aromatic Substitution Rates
7 Resonance Stabilization
8 Vibrational Analysis of Halogen Hydrides
9 Rotational Barrier in N-N-dimethylacetamide
10 Polarities of Small Molecules
11 Structures of Molecules which Exceed the Octet
12 Gas Phase Acidities of Binary pounds
13 Crystal Lattices and Close Packing Sites
14 Identification and Execution of Symmetry Operations
15 Infrared Spectra and Molecular Geometry
16 MOs of Simple Molecules
17 MOs of Second Period Diatomic Molecules
18 MOs of Octahedral Transition plexes
19 Relative Ligand Field Strengths
20 Stereoselectivity of Chiral Chelating Ligands…
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Changing face of chemistry
Arguably, more than half of all industrial chemists in the US are now employed in pharmaceuticals, biotechs or related business
Knowledge of protein structure and function is exploding
PDB in 1990 200 structures vs 18,000 today
Students are excited about the biotech century
General chemistry incorporating biochemistry
Biochemistry replacing general chemistry as first course in chemistry
Learning problems
What does a protein look like?
Which side is the “front”?
What’s wrong with a crystal structure?
How is sequence related to 3D structure?
What’s an active site?
What are conserved residues?
What is meant plementarity in docking?
Words are not enough.
Pictures and exploration are needed.
Four protein exercises –[free]
Importing and cleaning proteins
What does a protein look like?
What’s wrong with
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