Biochemistry Online: An Approach Based on Chemical Logic
Biochemistry Online: An Approach Based on Chemical Logic
Jsmol Files
1/7/16
The list below contains modeling tutorial files that are available from Biochemistry Online: An Approach Based on Chemical Logic. Some are links to outside files, but the majority have been created specifically for this course, some by students. Jsmol molecular modeling tutorials based on Javascript and HTML5 work best in Firefox and Safari. They work worst in Internet Explorer.
- List of Jmol for those interested in the Java versions.
- Jmol mouse commands
Optimal Browsers: from Eric Martz at http://bioinformatics.org/firstglance/fgij/notes.htm#browsers
| System | Browser | JSmol (No Java) | Jmol Java applet |
| Windows | Internet Explorer (notes) | Unworkably slow | Good |
| Edge (notes) | Very Slow | Not Supported | |
| Chrome (notes) | Slow | Not Supported | |
| Firefox (notes) | Best! | Good | |
| Opera (notes) | Slow | Good | |
| Maxthon (notes) | Slow | Good | |
| Mac OS X | Chrome (notes) | Slow | Not Supported |
| Firefox (notes) | Best! | Good* | |
| Safari (notes) | Best! | Good | |
| Opera (notes) | Slow | Not Working | |
| Maxthon (notes) | Best! | Not Supported |
Tables: Under construction as of 4/16
| Chapter 1: Lipids | ||||
| Jsmol: BC Online | PDB | Protopedia | First Glance | Others |
| Newman projections ethane | ChemTube 3D | |||
| Newman projection butane | ChemTube
3D With Movie Interactive |
|||
| di-18:0 PC | Link | Link | ||
| triacylglyceride | Link | Link | ||
| Micelle | Link | Link | ||
| Nonhydrated Bilayer | Link | Link | ||
| Human serum albumin complex with 18:0 | 1E7I | Link | Link | |
| Chapter 2 Protein Structure | ||||
| Jsmol: BC Online | PDB | Protopedia | First Glance | Others |
| Amino Acids | OMM- Cal Lutheran | |||
| RhoA - a cytoplasmic protein - The complexity of protein analysis | ||||
| An isolated helix from an Antifreeze Protein | ||||
| Twisted beta sheet from Arabinose Binding Protein | ||||
| Beta barrrel from triose phosphate isomerase | ||||
| Reverse Turn: Trypsin Inhibitor | ||||
| A protein with a buried nonpolar amino acid | ||||
| helix-loop-helix of the lambda Repressor | ||||
| helix-loop-helix (EF hand) from calmodulin | ||||
| beta-hairpin from bovine pancreatic trypsin inhibitor | ||||
| beta-helix-beta motif from triose phosphate isomerase | ||||
| cytochrome B562 | ||||
| met-myoglobin | ||||
| triose phosphate isomerase | ||||
|
Chapter 2: Protein Structure |
| Beta barrel from triose phosphate isomerase |
| Updated hexokinase Jmol14 (Java) | JSMol (HTML5) |
| Updated superoxide dismutase Jmol14 (Java) | JSMol (HTML5) |
| Updated human IgG1 antibody Jmol14 (Java) | JSMol (HTML5) |
| Updated retinol binding protein Jmol14 (Java) | JSMol (HTML5) |
| Updated RNase A Jmol14 (Java) | JSMol (HTML5) |
| Updated Apolactalbumin (w/o Ca2+)/Hololactalbumin Jmol14 (Java) | JSMol (HTML5) |
| Updated Engrailed homeodomain - denatured and native state Jmol14 (Java) | JSMol (HTML5) |
| Updated GroEL/ES Jmol14 (Java) | JSMol (HTML5) |
| Updated Cyclophilin Jmol14 (Java) | JSMol (HTML5) |
| Updated SecYEB Protein Translocase Jmol14 (Java) | JSMol (HTML5) |
| Updated Top7 - A designed 93 amino acid protein with a novel fold Jmol14 (Java) | JSMol (HTML5) |
|
Updated Prion Protein, Mad Cow Disease, and Mutations Jmol14 (Java) | JSMol (HTML5) |
|
Chapter 3: Carbohydrates |
| Updated β-D-glucopyranose Jmol14 (Java) | JSMol (HTML5) |
 D
Glucose |
|
Acetal
Formation |
|
Glycogen |
|
Amylose |
|
Amylopectin |
|
cellulose
|
|
Heparin |
| Updated Peptidoglycan glycosyl transferase Jmol14 (Java) | JSMol (HTML5) |
|
N-linked
Glycoprotein |
| Updated Oseltamivir: Neuramindase N1 complex Jmol14 (Java) | JSMol (HTML5) |
| Updated P-Selectin Lectin/EGF Domains (IG1Q) Jmol14 (Java) | JSMol (HTML5) |
|
Chapter 4: DNA, Genomics, and Proteomics |
|
DNA
Tutorial |
|
Chapter 5: Binding |
| Updated Avidin:Biotin Complex (1AVD) Jmol14 (Java) | JSMol (HTML5) |
| Updated Cu(I) Form Of E. Coli Cuer, A Copper Efflux Regulator Jmol14 (Java) | JSMol (HTML5) |
| Updated deoxy-heme and carbon monoxide-heme Jmol14 (Java) | JSMol (HTML5) |
| Updated Met-Myoglobin Jmol14 (Java) | JSMol (HTML5) |
| Updated Symmetry in Protein Oligomers (beta version with lots of work left to do) Jmol14 (Java) | JSMol (HTML5) (button no show) |
| Unliganded gp120 core (HIV viral protein) FIX |
| Updated Parainfluenza Virus 5F Protein Jmol14 (Java) | JSMol (HTML5) |
| Updated Simple DNA Tutorial Jmol14 (Java) | JSMol (HTML5) |
| Updated TATA Box Binding Protein Jmol14 (Java) | JSMol (HTML5) |
| Updated RNA Polymerase II/DNA/RNA complex Jmol14 (Java) | JSMol (HTML5) |
| Updated Auxin Receptor Jmol14 (Java) | JSMol (HTML5) Auxin Receptor |
| Updated Lambda Repressor: DNA complex | Jmol14 (Java) | JSMol (HTML5) |
| Updated Zif268:DNA Complex Jmol14 (Java) | JSMol (HTML5) |
| Updated Leucine Zipper Jmol14 (Java) | JSMol (HTML5) |
| Updated Methyl-CpG-Binding Domain of Human MBD1 in Complex with Methylated DNA Jmol14 (Java) | JSMol (HTML5) |
| Updated Nucleosome Jmol14 (Java) | JSMol (HTML5) |
| dsRNA (still figuring out to convert to JSMol) |
| Updated Dicer Jmol14 (Java) | JSMol (HTML5) Dicer |
| Updated TLR3:dsRNA complex Jmol14 (Java) | JSMol (HTML5) Needs updating |
| Updated Nf-Kb(P50)2 Complexed To A High- Affinity RNA Aptamer Jmol14 (Java) | JSMol (HTML5) |
|
Chapter 6: Transport and Kinetics |
| Updated Lactose Permease Jmol14 (Java) | JSMol (HTML5) |
| Updated Glycerol-3-Phosphate Transporter From E. Coli Jmol14 (Java) | JSMol (HTML5) |
|
Valinomycin |
|
Gramicidin |
|
Aquaporin |
| Updated Aquaporin Monomer Jmol14 (Java) | JSMol (HTML5) |
| Updated Maltoporin Transport Protein Jmol14 (Java) | JSMol (HTML5) |
|
Chapter 7: Catalysis |
| Updated Immunoglobulin 48G7 Germline Fab Antibody Complexed With Hapten 5-(Para-Nitrophenyl Phosphonate)-Pentanoic Acid Jmol14 (Java) JSMol (HTML5) |
| Updated Carboxypeptidase A Jmol14 (Java) | JSMol (HTML5) |
| Updated Chymotrypsin:D-Leu-L-Phe-p-fluorobenzylamde complex Jmol14 (Java) | JSMol (HTML5) |
| Updated Chymotrypin-Phenylethylboronate Inhibitor Complex Jmol14 (Java) | JSMol (HTML5) |
| Updated Comparison of Chymotrypin and Subtilisin Jmol14 (Java) | JSMol (HTML5) |
| Updated E. Coli GlpG rhomboid intramembrane protease Jmol14 (Java) | JSMol (HTML5) |
| Updated Mammalian Proteasome - (1IRU) Jmol14 (Java) | JSMol (HTML5) |
|
THIAMIN
DIPHOSPHATE DEPENDENT ENZYME PYRUVATE DECARBOXYLASE (1pyd) (go
to left hand Display Molecule, choose Jmol viewer). |
| Updated Glyceraldehyde-3-phosphate dehydrogenase (NAD) Jmol14 (Java) | JSMol (HTML5) |
|
Tyrosine
Aminotransferase Jmol (from PDB) |
| Updated Self-splicing Group I intron with both exons Jmol14 (Java) | JSMol (HTML5) |
| Updated L1 Ligase Ribozyme Jmol14 (Java) | JSMol (HTML5) Not done; Fix |
| Puckering in ribose and deoxyribose Not updated Fix |
| Comparison of ds DNA forms Not updated Fix Calluthan A B Z DNA Jsmol |
| Comparison of ds DNA and Not updated Fix |
|
Chapter 8: Oxidative Phosphorylation |
| Updated Adenine DNA glycosylase:8-oxyG DNA complex Jmol14 (Java) | JSMol (HTML5) |
| Updated Flavin dehydrogenase Jmol14 (Java) | JSMol (HTML5) |
| Updated Estrogen Receptor:Tamoxifen Complex Jmol14 (Java) | JSMol (HTML5) |
| Updated Cytochrome P450cam Jmol14 (Java) | JSMol (HTML5) |
|
Cyclooxygenase
I and II |
| Updated Cytochrome C Oxidase Jmol14 (Java) | JSMol (HTML5) |
| Updated ATP Jmol14 (Java) | JSMol (HTML5) | ADP Jmol14 (Java) | JSMol (HTML5) |
| Updated Glyceraldehyde-3-phosphate dehydrogenase (NAD) Jmol14 (Java) | JSMol (HTML5) |
| Updated Cytochrome C Oxidase Jmol14 (Java) | JSMol (HTML5) |
| Updated Succinate Dehydrogenase (Complex II) Jmol14 (Java) | JSMol (HTML5) |
| Updated Light Harvesting Complex from Spinach 1RWT Jmol14 (Java) | JSMol (HTML5) |
| Updated Detailed Photosystem II from S. elongatus Jmol14 (Java) | JSMol (HTML5) |
| Updated Photosystem I: A Photosynthetic Reaction Center and Core Antenna System From Cyanobacteria 1JBO Jmol14 (Java) | JSMol (HTML5) |
|
Chapter 9: Energy and Signal Transduction |
| Updated Bacteriorhodopsin Crystallized From Bicelles Jmol14 (Java) | JSMol (HTML5) | LMW-PTP isoform A |
| Updated EmrE multidrug resistance transporter Jmol14 (Java) | JSMol (HTML5) |
| Updated Acetylcholine Receptor Pore Jmol14 (Java) | JSMol (HTML5) (1OED) |
| Potassium Channel Not updated; Needs work |
| Updated Mammalian Voltage-Dependent Shaker Family Potassium Channel Jmol14 (Java) | JSMol (HTML5) |
| Updated Chloride Channel Jmol14 (Java) | JSMol (HTML5) |
| NEW Low molecular weight protein tyrosine phsophatase Jmol14 (Java) | JSMol (HTML5) |
| Updated Gs-alpha/adenylate cyclase complex Jmol14 (Java) | JSMol (HTML5) |
| Updated Beta andrenergic receptor Jmol14 (Java) | JSMol (HTML5) |
| Updated Beta andrenergic receptor:Gs Complex Jmol14 (Java) | JSMol (HTML5) |
| Updated Melancortin 4 Receptor Jmol14 (Java) | JSMol (HTML5) |
| Updated AMP-dependent Protein Kinase (AMPK) Jmol14 (Java) | JSMol (HTML5) |
General Sites
General Jmol Sites
- Molecules in Motion
- JMol
- Jmol web sites
- Jmol demos
- Awesome tutorial!
- 2nd awesome tutorial on surfaces
- Jmol 11.4 script commands
- Online Molecule Museum
- Organic
- Another organic chem site
- Jmol Organic mechanisms
- Jmol Documentation and Websites
- Jmol Documentation
- Updates to Jmol
- Popup window for testing Jmol commands
- Molecular Science Lab: CHO, Lipid, Protein structures
- MolViz
- MolViz Top 5
- Protopedia: The collaborative, 3D encyclopedia of proteins and other molecules
- Jmol tutorial templates
- Jmol autoring template
Navigation
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Biochemistry Online by Henry Jakubowski is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.