| Topic
|
Subject |
| 1 |
Background
Enthalpy, entropy and free energy |
| 2
|
Molecular Interactions Web Site -----------------------------------> Water Pymol Script -----------------------------------> GC Base Pair Pymol Script -----------------------------------> Short Range Repulsion Pymol Script Ions -----------------------------------> Electrostatic Interactions Pymol Script The hydrophobic effect Small molecule library |
| 3
|
Protein monomers and oligomers
Amino acids The peptide bond -----------------------------------> Peptide Bond Pymol Script Φ/Ψ torsion angles -----------------------------------> Φ/Ψ Pymol Script |
| 4
|
Protein secondary structure
α-Helix -----------------------------------> α-Helix Pymol Script β-Sheet -----------------------------------> Parallel β-Sheet Pymol Script -----------------------------------> Antiparallel β-Sheet Pymol Script Loops and turns |
| 5
|
Protein Folds
-----------------------------------> Protein Folds Pymol Script Fibrous proteins -----------------------------------> Collagen Pymol Script α-Helical proteins -----------------------------------> Albumin Pymol Script -----------------------------------> Myoglobin Pymol Script -----------------------------------> Hemoglobin Pymol Script -----------------------------------> Seven Transmembrane α-Helices Pymol Script α-Helical/β-Sheet proteins -----------------------------------> Carboxypeptidase Pymol Script -----------------------------------> Ribonuclease A Pymol Script Anti-parallel β-sheet proteins -----------------------------------> Porin Pymol Script -----------------------------------> Peptide Amyloid Pymol Script -----------------------------------> Full Length Amyloid Pymol Script parallel β-sheet proteins -----------------------------------> HMW1 Adhesin Pymol Script -----------------------------------> Groel -----------------------------------> Evolution of Folding |
| 6
|
Protein/Metal Interactions
Metals (radii, coordinate numbers, etc) -----------------------------------> Calmodulin Pymol Script Potassium Channel |
| 7
|
Protein/Nucleotide Interactions
Rossman Fold |
| 8
|
Bases, Nucleosides and Nucleotides
ribose/deoxyribose -----------------------------------> Syn/Anti Pymol Script -----------------------------------> Sugar Pucker Pymol Script bases base pairs, triplets and quartets ----------------------------------> Hoogsteen Base Pair Pymol Script |
| 9a
|
DNA Structure
-----------------------------------> B-Form DNA Pymol Script -----------------------------------> Quadruplex DNA Pymol Script phosphodiester backbone -----------------------------------> DNA Torsion Angle Pymol Script -----------------------------------> Triplex Pymol Script A,B,Z conformation Supercoiling |
| 9b
|
RNA Structure
-----------------------------------> ATP Pymol Script -----------------------------------> A-Form RNA Pymol Script GNRA Tetraloops -----------------------------------> GNRA Tetraloop Pymol Script ---------------------------------------------> coordinates for 20 GNRA tetraloops Kink-Turns -----------------------------------> Kink-Turn Pymol Script tRNA -----------------------------------> tRNA Pymol Script Ribosome -----------------------------------> Small Subunit Pymol Script -----------------------------------> Thermus Thermophilus Ribosome Pymol Script motifs |
| 10
|
Interactions of nucleic acids with small molecules
Water -----------------------------------> Spine of Hydration Pymol Script Magnesium Spermine Minor groove binders Intercalators and Bis-intercalators |
|
11a
|
Carbohydrate
Images and Coordinates ----------------------------------->Cellulose Pymol Script |
| 11b
|
Interactions of nucleic acids with proteins
----------------------------------->Toll-like Receptor Pymol Script -----------------------------------> HU Protein Pymol Script -----------------------------------> DNA Ligase Pymol Script Nucleosome -----------------------------------> Nucleosome Pymol Script -----------------------------------> P22 Repressor: HTH Pymol Script -----------------------------------> TBP Pymol Script -----------------------------------> Yeast RNA Pol II Pymol Script Zinc Fingers -----------------------------------> Zinc Finger Pymol Script ZIP Helix-loop-helix β-ribbon Restriction and Modification Enzymes -----------------------------------> Bam HI Pymol Script -----------------------------------> BGL II Pymol Script -----------------------------------> Eco RI Pymol Script -----------------------------------> Fok I Pymol Script -----------------------------------> Not I Pymol Script -----------------------------------> Pvu II Pymol Script tRNA synthetases -----------------------------------> Class I: Glutamyl-tRNA sythetase Pymol Script Rev response element/rev peptide Polymerases -----------------------------------> Bacillus DNA Polymerase I Pymol Script |
| 11c
|
Viruses & Phages
----------------------------------->QΒ VLP Pymol Script |
| 12
|
Enzymes and Catalysis
Serine Proteases -----------------------------------> Trypsin TS Analog Pymol Script -----------------------------------> Hexokinase Pymol Script -----------------------------------> Succinyl-CoA Synthetase Pymol Script -----------------------------------> Amidoribosyl Transferase Pymol Script |
| 13
|
Databases
PDB, CSD, PubMed How to use the PDB |
| 14
|
Display and Manipulation
Student Pymol Download Mac PC Pymol Documentation |
